1
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Shen J, Liu J, Yu S, Yu Y, Huang C, Xiong X, Yue J, Dai Q. Diaminodiacid bridge improves enzymatic and in vivo inhibitory activity of peptide CPI-1 against botulinum toxin serotype A. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.03.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Lam KH, Sikorra S, Weisemann J, Maatsch H, Perry K, Rummel A, Binz T, Jin R. Structural and biochemical characterization of the protease domain of the mosaic botulinum neurotoxin type HA. Pathog Dis 2018; 76:4982781. [PMID: 29688327 DOI: 10.1093/femspd/fty044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/20/2018] [Indexed: 11/13/2022] Open
Abstract
The extreme toxicity of botulinum neurotoxins (BoNTs) relies on their specific cleavage of SNARE proteins, which eventually leads to muscle paralysis. One newly identified mosaic toxin, BoNT/HA (aka H or FA), cleaves VAMP-2 at a unique position between residues L54 and E55, but the molecular basis underlying VAMP-2 recognition of BoNT/HA remains poorly characterized. Here, we report a ∼2.09 Å resolution crystal structure of the light chain protease domain of BoNT/HA (LC/HA). Structural comparison between LC/HA and LC of BoNT/F1 (LC/F1) reveals distinctive hydrophobic and electrostatic features near the active sites, which may explain their different VAMP-2 cleavage sites. When compared to BoNT/F5 that cleaves VAMP-2 at the same site as BoNT/HA, LC/HA displays higher affinity for VAMP-2, which could be caused by their different surface charge properties surrounding a VAMP-2 exosite-binding cleft. Furthermore, systematic mutagenesis studies on VAMP-2 and structural modeling demonstrate that residues R47 to K59 spanning the cleavage site in VAMP-2 may adopt a novel extended conformation when interacting with LC/HA and LC/F5. Taken together, our structure provides new insights into substrate recognition of BoNT/HA and paves the way for rational design of small molecule or peptide inhibitors against LC/HA.
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Affiliation(s)
- Kwok-Ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697 USA
| | - Stefan Sikorra
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Jasmin Weisemann
- Institut für Toxikologie, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Hannah Maatsch
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andreas Rummel
- Institut für Toxikologie, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Thomas Binz
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697 USA
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3
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Mansfield MJ, Doxey AC. Genomic insights into the evolution and ecology of botulinum neurotoxins. Pathog Dis 2018; 76:4978416. [PMID: 29684130 DOI: 10.1093/femspd/fty040] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/17/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael J Mansfield
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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4
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Bremer PT, Pellett S, Carolan JP, Tepp WH, Eubanks LM, Allen KN, Johnson EA, Janda KD. Metal Ions Effectively Ablate the Action of Botulinum Neurotoxin A. J Am Chem Soc 2017; 139:7264-7272. [PMID: 28475321 PMCID: PMC5612488 DOI: 10.1021/jacs.7b01084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) causes a debilitating and potentially fatal illness known as botulism. The toxin is also a bioterrorism threat, yet no pharmacological antagonist to counteract its effects has reached clinical approval. Existing strategies to negate BoNT/A intoxication have looked to antibodies, peptides, or organic small molecules as potential therapeutics. In this work, a departure from the traditional drug discovery mindset was pursued, in which the enzyme's susceptibility to metal ions was exploited. A screen of a series of metal salts showed marked inhibitory activity of group 11 and 12 metals against the BoNT/A light chain (LC) protease. Enzyme kinetics revealed that copper (I) and (II) cations displayed noncompetitive inhibition of the LC (Ki ≈ 1 μM), while mercury (II) cations were 10-fold more potent. Crystallographic and mutagenesis studies elucidated a key binding interaction between Cys165 on BoNT/A LC and the inhibitory metals. As potential copper prodrugs, ligand-copper complexes were examined in a cell-based model and were found to prevent BoNT/A cleavage of the endogenous protein substrate, SNAP-25, even at low μM concentrations of complexes. Further investigation of the complexes suggested a bioreductive mechanism causing intracellular release of copper, which directly inhibited the BoNT/A protease. In vivo experiments demonstrated that copper (II) dithiocarbamate and bis(thiosemicarbazone) complexes could delay BoNT/A-mediated lethality in a rodent model, indicating their potential for treating the harmful effects of BoNT/A intoxication. Our studies illustrate that metals can be therapeutically viable enzyme inhibitors; moreover, enzymes that share homology with BoNT LCs may be similarly targeted with metals.
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Affiliation(s)
- Paul T. Bremer
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, Wisconsin 53706, USA
| | - James P. Carolan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - William H. Tepp
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, Wisconsin 53706, USA
| | - Lisa M. Eubanks
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Eric A. Johnson
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, Wisconsin 53706, USA
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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5
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Pirazzini M, Rossetto O. Challenges in searching for therapeutics against Botulinum Neurotoxins. Expert Opin Drug Discov 2017; 12:497-510. [DOI: 10.1080/17460441.2017.1303476] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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Yalamanchili C, Manda VK, Chittiboyina AG, Guernieri RL, Harrell WA, Webb RP, Smith LA, Khan IA. Utilizing Ayurvedic literature for the identification of novel phytochemical inhibitors of botulinum neurotoxin A. JOURNAL OF ETHNOPHARMACOLOGY 2017; 197:211-217. [PMID: 27469199 DOI: 10.1016/j.jep.2016.07.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ayurveda, an ancient holistic system of health care practiced on the Indian subcontinent, utilizes a number of multi-plant formulations and is considered by many as a potential source for novel treatments, as well as the identification of new drugs. Our aim is to identify novel phytochemicals for the inhibition of bacterial exotoxin, botulinum neurotoxin A (BoNT/A) based on Ayurvedic literature. BoNT/A is released by Clostridium species, which when ingested, inhibits the release of acetylcholine by concentrating at the neuromuscular junction and causes flaccid paralysis, resulting in a condition termed as botulism, and may also lead to death due to respiratory arrest. METHODS Fifteen plants were selected from the book 'Diagnosis and treatment of diseases in Ayurveda' by Vaidya Bhagwan Dash and Lalitesh Kashyap, based on their frequency of use in the formulations used for the treatment of six diseases with neuromuscular symptoms similar to botulism. Phytochemicals from these plants were screened using in silico, and in vitro methods. Structures of 570 reported phytochemicals from 14 plants were docked inside six reported BoNT/A light chain crystal structures using ensemble docking module in Maestro (Schrödinger, LLE). RESULTS From the docking scores and structural diversity, nine compounds including acoric acid 1, three flavonoids, three coumarins derivatives, one kava lactone were selected and screened using an in vitro HPLC-based protease assay. The bioassay results showed that several compounds possess BoNT/A LC inhibition of 50-60% when compared to positive controls NSC 84094 and CB7967495 (80-95%). CONCLUSION Further testing of the active compounds identified from Ayurvedic literature and structure-activity studies of acoric acid 1 using more sensitive bioassays is under way. The identification of acoric acid 1, a novel scaffold against BoNT/A, exemplifies the utility of Ayurvedic literature for the discovery of novel drug leads.
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Affiliation(s)
- Chinni Yalamanchili
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, The University of Mississippi, University, MS 38677, USA; Divison of Pharmacognosy, Department of BioMolecular Sciences, The University of Mississippi, University, MS 38677, USA
| | - Vamshi K Manda
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, The University of Mississippi, University, MS 38677, USA
| | - Amar G Chittiboyina
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, The University of Mississippi, University, MS 38677, USA
| | - Rebecca L Guernieri
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA
| | - William A Harrell
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA
| | - Robert P Webb
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA
| | - Leonard A Smith
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA
| | - Ikhlas A Khan
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, The University of Mississippi, University, MS 38677, USA; Divison of Pharmacognosy, Department of BioMolecular Sciences, The University of Mississippi, University, MS 38677, USA.
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8
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Bremer PT, Adler M, Phung CH, Singh AK, Janda KD. Newly Designed Quinolinol Inhibitors Mitigate the Effects of Botulinum Neurotoxin A in Enzymatic, Cell-Based, and ex Vivo Assays. J Med Chem 2017; 60:338-348. [PMID: 27966961 DOI: 10.1021/acs.jmedchem.6b01393] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Botulinum neurotoxin A (BoNT/A) is one of the most deadly toxins and is the etiological agent of the potentially fatal condition, botulism. Herein, we investigated 8-hydroxyquinoline (quinolin-8-ol) as a potential inhibitor scaffold for preventing the deadly neurochemical effects of the toxin. Quinolinols are known chelators that can disrupt the BoNT/A metalloprotease zinc-containing active site, thus impeding its proteolysis of the endogenous protein substrate, synaptosomal-associated protein 25 (SNAP-25). By use of this information, the structure-activity relationship (SAR) of the quinolinol-5-sulfonamide scaffold was explored through preparation of a crude sulfonamide library and evaluation of the library in a BoNT/A LC enzymatic assay. Potency optimization of the sulfonamide hit compounds was undertaken as informed by docking studies, granting a lead compound with a submicromolar Ki. These quinolinol analogues demonstrated inhibitory activity in a cell-based model for SNAP-25 cleavage and an ex vivo assay for BoNT/A-mediated muscle paralysis.
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Affiliation(s)
- Paul T Bremer
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael Adler
- Neurobehavioral Toxicology Branch, Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense , 2900 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400, United States
| | - Cecilia H Phung
- Neurobehavioral Toxicology Branch, Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense , 2900 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400, United States
| | - Ajay K Singh
- Neurobehavioral Toxicology Branch, Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense , 2900 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400, United States
| | - Kim D Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Bremer PT, Xue S, Janda KD. Picolinic acids as β-exosite inhibitors of botulinum neurotoxin A light chain. Chem Commun (Camb) 2016; 52:12521-12524. [PMID: 27722252 PMCID: PMC5085802 DOI: 10.1039/c6cc06749b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In developing small-molecule inhibitors of botulinum neurotoxin serotype A light chain (BoNT/A LC), substituted picolinic acids were identified. Extensive investigation into the SAR of the picolinic acid scaffold revealed 5-(1-butyl-4-chloro-1H-indol-2-yl)picolinic acid (CBIP), which possessed low micromolar activity against BoNT/A. Kinetic and docking studies demonstrated binding of CBIP to the β-exosite: a largely unexplored site on the LC that holds therapeutic relevance for botulism treatment.
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Affiliation(s)
- Paul T Bremer
- Departments of Chemistry, Immunology and Microbial Sciences, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.
| | - Song Xue
- Departments of Chemistry, Immunology and Microbial Sciences, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.
| | - Kim D Janda
- Departments of Chemistry, Immunology and Microbial Sciences, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.
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10
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Kumar G, Agarwal R, Swaminathan S. Small molecule non-peptide inhibitors of botulinum neurotoxin serotype E: Structure-activity relationship and a pharmacophore model. Bioorg Med Chem 2016; 24:3978-3985. [PMID: 27353886 DOI: 10.1016/j.bmc.2016.06.036] [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] [Received: 09/08/2015] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 10/21/2022]
Abstract
Botulinum neurotoxins (BoNTs) are the most poisonous biological substance known to humans. They cause flaccid paralysis by blocking the release of acetylcholine at the neuromuscular junction. Here, we report a number of small molecule non-peptide inhibitors of BoNT serotype E. The structure-activity relationship and a pharmacophore model are presented. Although non-peptidic in nature, these inhibitors mimic key features of the uncleavable substrate peptide Arg-Ile-Met-Glu (RIME) of the SNAP-25 protein. Among the compounds tested, most of the potent inhibitors bear a zinc-chelating moiety connected to a hydrophobic and aromatic moiety through a carboxyl or amide linker. All of them show low micromolar IC50 values.
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Affiliation(s)
- Gyanendra Kumar
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Rakhi Agarwal
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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11
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Zhou Y, McGillick BE, Teng YHG, Haranahalli K, Ojima I, Swaminathan S, Rizzo RC. Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity. Bioorg Med Chem 2016; 24:4875-4889. [PMID: 27543389 DOI: 10.1016/j.bmc.2016.07.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/15/2016] [Accepted: 07/16/2016] [Indexed: 11/15/2022]
Abstract
Botulinum neurotoxins (BoNT) are among the most poisonous substances known, and of the 7 serotypes (A-G) identified thus far at least 4 can cause death in humans. The goal of this work was identification of inhibitors that specifically target the light chain catalytic site of the highly pathogenic but lesser-studied E serotype (BoNT/E). Large-scale computational screening, employing the program DOCK, was used to perform atomic-level docking of 1.4 million small molecules to prioritize those making favorable interactions with the BoNT/E site. In particular, 'footprint similarity' (FPS) scoring was used to identify compounds that could potentially mimic features on the known substrate tetrapeptide RIME. Among 92 compounds purchased and experimentally tested, compound C562-1101 emerged as the most promising hit with an apparent IC50 value three-fold more potent than that of the first reported BoNT/E small molecule inhibitor NSC-77053. Additional analysis showed the predicted binding pose of C562-1101 was geometrically and energetically stable over an ensemble of structures generated by molecular dynamic simulations and that many of the intended interactions seen with RIME were maintained. Several analogs were also computationally designed and predicted to have further molecular mimicry thereby demonstrating the potential utility of footprint-based scoring protocols to help guide hit refinement.
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Affiliation(s)
- Yuchen Zhou
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - Brian E McGillick
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, NY 11794, United States; Biology Department, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Yu-Han Gary Teng
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794, United States; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States
| | | | - Iwao Ojima
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794, United States; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States
| | | | - Robert C Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States; Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794, United States; Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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Guo J, Wang J, Gao S, Ji B, Waichi Chan E, Chen S. Substrate-based inhibitors exhibiting excellent protective and therapeutic effects against Botulinum Neurotoxin A intoxication. Sci Rep 2015; 5:16981. [PMID: 26584873 PMCID: PMC4653808 DOI: 10.1038/srep16981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/22/2015] [Indexed: 12/18/2022] Open
Abstract
Potent inhibitors to reverse Botulinum neurotoxins (BoNTs) activity in neuronal cells are currently not available. A better understanding of the substrate recognition mechanism of BoNTs enabled us to design a novel class of peptide inhibitors which were derivatives of the BoNT/A substrate, SNAP25. Through a combination of in vitro, cellular based, and in vivo mouse assays, several potent inhibitors of approximately one nanomolar inhibitory strength both in vitro and in vivo have been identified. These compounds represent the first set of inhibitors that exhibited full protection against BoNT/A intoxication in mice model with undetectable toxicity. Our findings validated the hypothesis that a peptide inhibitor targeting the two BoNT structural regions which were responsible for substrate recognition and cleavage respectively could exhibit excellent inhibitory effect, thereby providing insight on future development of more potent inhibitors against BoNTs.
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Affiliation(s)
- Jiubiao Guo
- Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, People’s Republic of China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, People’s Republic of China
| | - Bin Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, People’s Republic of China
| | - Edward Waichi Chan
- Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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Kumaran D, Adler M, Levit M, Krebs M, Sweeney R, Swaminathan S. Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: Insights from X-ray crystallography. Bioorg Med Chem 2015; 23:7264-73. [PMID: 26522088 DOI: 10.1016/j.bmc.2015.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 10/16/2015] [Indexed: 10/22/2022]
Abstract
The seven antigenically distinct serotypes (A-G) of botulinum neurotoxin (BoNT) are responsible for the deadly disease botulism. BoNT serotype A (BoNT/A) exerts its lethal action by cleaving the SNARE protein SNAP-25, leading to inhibition of neurotransmitter release, flaccid paralysis and autonomic dysfunction. BoNTs are dichain proteins consisting of a ∼ 100 kDa heavy chain and a ∼ 50 kDa light chain; the former is responsible for neurospecific binding, internalization and translocation, and the latter for cleavage of neuronal SNARE proteins. Because of their extreme toxicity and history of weaponization, the BoNTs are regarded as potential biowarfare/bioterrorism agents. No post-symptomatic therapeutic interventions are available for BoNT intoxication other than intensive care; therefore it is imperative to develop specific antidotes against this neurotoxin. To this end, a cyclic peptide inhibitor (CPI-1) was evaluated in a FRET assay for its ability to inhibit BoNT/A light chain (Balc). CPI was found to be highly potent, exhibiting a Ki of 12.3 nM with full-length Balc448 and 39.2 nM using a truncated crystallizable form of the light chain (Balc424). Cocrystallization studies revealed that in the Balc424-CPI-1 complex, the inhibitor adopts a helical conformation, occupies a high percentage of the active site cavity and interacts in an amphipathic manner with critical active site residues. The data suggest that CPI-1 prevents SNAP-25 from accessing the Balc active site by blocking both the substrate binding path at the surface and the Zn(2+) binding region involved in catalysis. This differs from linear peptide inhibitors described to date which block only the latter.
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Affiliation(s)
- Desigan Kumaran
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Michael Adler
- Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense (USAMRICD), Aberdeen Proving Ground, MD 21010, United States.
| | - Matthew Levit
- Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense (USAMRICD), Aberdeen Proving Ground, MD 21010, United States
| | - Michael Krebs
- Analytical Toxicology Division, U.S. Army Medical Research Institute of Chemical Defense (USAMRICD), Aberdeen Proving Ground, MD 21010, United States
| | - Richard Sweeney
- Research Division, USAMRICD, Aberdeen Proving Ground, MD 21010, United States
| | - Subramanyam Swaminathan
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
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14
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Computer-aided identification, synthesis, and biological evaluation of novel inhibitors for botulinum neurotoxin serotype A. Bioorg Med Chem 2015; 23:5489-95. [DOI: 10.1016/j.bmc.2015.07.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/13/2015] [Accepted: 07/19/2015] [Indexed: 11/24/2022]
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16
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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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Bremer PT, Hixon MS, Janda KD. Benzoquinones as inhibitors of botulinum neurotoxin serotype A. Bioorg Med Chem 2014; 22:3971-81. [PMID: 24984937 DOI: 10.1016/j.bmc.2014.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 02/06/2023]
Abstract
Although botulinum neurotoxin serotype A (BoNT/A) is known for its use in cosmetics, it causes a potentially fatal illness, botulism, and can be used as a bioterror weapon. Many compounds have been developed that inhibit the BoNTA zinc-metalloprotease light chain (LC), however, none of these inhibitors have advanced to clinical trials. In this study, a fragment-based approach was implemented to develop novel covalent inhibitors of BoNT/A LC. First, electrophilic fragments were screened against BoNT/A LC, and benzoquinone (BQ) derivatives were found to be active. In kinetic studies, BQ compounds acted as irreversible inhibitors that presumably covalently modify cysteine 165 of BoNT/A LC. Although most BQ derivatives were highly reactive toward glutathione in vitro, a few compounds such as natural product naphthazarin displayed low thiol reactivity and good BoNT/A inhibition. In order to increase the potency of the BQ fragment, computational docking studies were employed to elucidate a scaffold that could bind to sites adjacent to Cys165 while positioning a BQ fragment at Cys165 for covalent modification; 2-amino-N-arylacetamides met these criteria and when linked to BQ displayed at least a 20-fold increase in activity to low μM IC₅₀ values. Unlike BQ alone, the linked-BQ compounds demonstrated only weak irreversible inhibition and therefore acted mainly as non-covalent inhibitors. Further kinetic studies revealed a mutual exclusivity of BQ covalent inactivation and competitive inhibitor binding to sites adjacent to Cys165, refuting the viability of the current strategy for developing more potent irreversible BoNT/A inhibitors. The highlights of this study include the discovery of BQ compounds as irreversible BoNT/A inhibitors and the rational design of low μM IC50 competitive inhibitors that depend on the BQ moiety for activity.
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Affiliation(s)
- Paul T Bremer
- Departments of Chemistry and Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark S Hixon
- Discovery Biology, Takeda San Diego, Inc., 10410 Science Center Drive, San Diego, CA 92121, USA
| | - Kim D Janda
- Departments of Chemistry and Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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18
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Mizanur RM, Stafford RG, Ahmed SA. Cleavage of SNAP25 and its shorter versions by the protease domain of serotype A botulinum neurotoxin. PLoS One 2014; 9:e95188. [PMID: 24769566 PMCID: PMC4000213 DOI: 10.1371/journal.pone.0095188] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/25/2014] [Indexed: 11/18/2022] Open
Abstract
Various substrates, catalysts, and assay methods are currently used to screen inhibitors for their effect on the proteolytic activity of botulinum neurotoxin. As a result, significant variation exists in the reported results. Recently, we found that one source of variation was the use of various catalysts, and have therefore evaluated its three forms. In this paper, we characterize three substrates under near uniform reaction conditions using the most active catalytic form of the toxin. Bovine serum albumin at varying optimum concentrations stimulated enzymatic activity with all three substrates. Sodium chloride had a stimulating effect on the full length synaptosomal-associated protein of 25 kDa (SNAP25) and its 66-mer substrates but had an inhibitory effect on the 17-mer substrate. We found that under optimum conditions, full length SNAP25 was a better substrate than its shorter 66-mer or 17-mer forms both in terms of kcat, Km, and catalytic efficiency kcat/Km. Assay times greater than 15 min introduced large variations and significantly reduced the catalytic efficiency. In addition to characterizing the three substrates, our results identify potential sources of variations in previous published results, and underscore the importance of using well-defined reaction components and assay conditions.
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Affiliation(s)
- Rahman M. Mizanur
- Department of Cell Biology and Biochemistry, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Robert G. Stafford
- Department of Cell Biology and Biochemistry, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - S. Ashraf Ahmed
- Department of Cell Biology and Biochemistry, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
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19
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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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20
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Mizanur RM, Frasca V, Swaminathan S, Bavari S, Webb R, Smith LA, Ahmed SA. The C terminus of the catalytic domain of type A botulinum neurotoxin may facilitate product release from the active site. J Biol Chem 2013; 288:24223-33. [PMID: 23779108 DOI: 10.1074/jbc.m113.451286] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Botulinum neurotoxins are the most toxic of all compounds. The toxicity is related to a poor zinc endopeptidase activity located in a 50-kDa domain known as light chain (Lc) of the toxin. The C-terminal tail of Lc is not visible in any of the currently available x-ray structures, and it has no known function but undergoes autocatalytic truncations during purification and storage. By synthesizing C-terminal peptides of various lengths, in this study, we have shown that these peptides competitively inhibit the normal catalytic activity of Lc of serotype A (LcA) and have defined the length of the mature LcA to consist of the first 444 residues. Two catalytically inactive mutants also inhibited LcA activity. Our results suggested that the C terminus of LcA might interact at or near its own active site. By using synthetic C-terminal peptides from LcB, LcC1, LcD, LcE, and LcF and their respective substrate peptides, we have shown that the inhibition of activity is specific only for LcA. Although a potent inhibitor with a Ki of 4.5 μm, the largest of our LcA C-terminal peptides stimulated LcA activity when added at near-stoichiometric concentration to three versions of LcA differing in their C-terminal lengths. The result suggested a product removal role of the LcA C terminus. This suggestion is supported by a weak but specific interaction determined by isothermal titration calorimetry between an LcA C-terminal peptide and N-terminal product from a peptide substrate of LcA. Our results also underscore the importance of using a mature LcA as an inhibitor screening target.
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Affiliation(s)
- Rahman M Mizanur
- Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
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21
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Šilhár P, Silvaggi NR, Pellett S, Čapková K, Johnson EA, Allen KN, Janda KD. Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies. Bioorg Med Chem 2012; 21:1344-8. [PMID: 23340139 DOI: 10.1016/j.bmc.2012.12.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/01/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
Abstract
Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a series of hydroxamates derived from 1-adamantylacetohydroxamic acid (3a) were prepared. From this group of compounds, an improved potency of about 17-fold was observed for two derivatives. Detailed mechanistic studies on these structures revealed a competitive inhibition model, with a K(i)=27 nM, which makes these compounds some of the most potent small molecule, non-peptidic BoNT/A LC inhibitors reported to date.
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Affiliation(s)
- Peter Šilhár
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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22
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Kitamura K, Komatsu M, Biyani M, Futakami M, Kawakubo T, Yamamoto K, Nishigaki K. Proven in vitro evolution of protease cathepsin E-inhibitors and -activators at pH 4.5 using a paired peptide method. J Pept Sci 2012; 18:711-9. [PMID: 23109368 DOI: 10.1002/psc.2453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 07/08/2012] [Accepted: 08/20/2012] [Indexed: 12/25/2022]
Abstract
Improving a particular function of molecules is often more difficult than identifying such molecules ab initio. Here, a method to acquire higher affinity and/or more functional peptides was developed as a progressive library selection method. The primary library selection products were utilized to build a secondary library composed of blocks of 4 amino acids, of which selection led to peptides with increased activity. These peptides were further converted to randomly generate paired peptides. Cathepsin E-inhibitors thus obtained exhibited the highest activities and affinities (pM order). This was also the case with cathepsin E-activating peptides, proving the methodological effectiveness. The primary, secondary, and tertiary library selections can be regarded as module-finding, module-shuffling, and module-pairing, respectively, which resembles the progression of the natural evolution of proteins. The mode of peptide binding to their target proteins is discussed in analogy to antibodies and epitopes of an antigen.
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Affiliation(s)
- Koichiro Kitamura
- Janusys Corporation, #508, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, 338-8570, Japan; Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-ku, Saitama City, Saitama, 338-0001, Japan
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23
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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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24
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Eichhorn T, Dolimbek BZ, Deeg K, Efferth T, Atassi MZ. Inhibition in vivo of the activity of botulinum neurotoxin A by small molecules selected by virtual screening. Toxicon 2012; 60:1180-90. [PMID: 22960451 DOI: 10.1016/j.toxicon.2012.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
Abstract
To search for small molecular size inhibitors of botulinum neurotoxin A (BoNT/A) endopeptidase activity, we have screened the NCI library containing about 1 million structures against the substrate binding pocket of BoNT/A. Virtual screening (VS) was performed with the software Glide (Grid-based ligand docking energetics) and the findings were confirmed by AutoDock. Ten compounds were found that had favorable energetic and glide criteria and 5 of these compounds were selected for their ability to protect mice in vivo against a lethal dose of BoNT/A. Each compound was incubated at different molar excesses with a lethal dose of the toxin and then the mixture injected intravenously into mice. At 4690 M excess, compounds NSC94520 and NSC99639 protected all (100%) the mice from lethal toxicity. Compounds NSC48461 and NSC627733 gave 75% protection. Compound NSC348884 showed the least inhibition of toxicity allowing only a fraction (25%) of the mice to survive challenge with a lethal dose; and in the case of the mice that did not survive there was a considerable delay of mortality. At 2400 M excess compounds NSC94520 remained fully protective while and NSC99639 afforded 75% protection and at 1200 M excess each of these two compounds gave 50% protection. The two compounds gave no protection at 600 or less molar excess. When each compound was administered intravenously at 4690 M excess at different times (from 1 h to 6 h) after the intravenous injection of the active toxin, none of the compounds was able to protect the animals from toxicity. The findings show the value of VS in identifying potential inhibitors of the toxin for further development and improvement.
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Affiliation(s)
- Tolga Eichhorn
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
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25
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Ho M, Goh CH, Brothers MC, Wang S, Young RL, Ou Y, Lui JNM, Kalafatis M, Lan X, Wolf AE, Rienstra CM, Wilson BA. Glycine insertion at protease cleavage site of SNAP25 resists cleavage but enhances affinity for botulinum neurotoxin serotype A. Protein Sci 2012; 21:318-26. [PMID: 22170566 DOI: 10.1002/pro.2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The light chain of botulinum neurotoxin A (BoNT/A-LC) is a Zn-dependent protease that specifically cleaves SNAP25 of the SNARE complex, thereby impairing vesicle fusion and neurotransmitter release at neuromuscular junctions. The C-terminus of SNAP25 (residues 141-206) retains full activity for BoNT/A-LC-catalyzed cleavage at P1-P1' (Gln197-Arg198). Using the structure of a complex between the C-terminus of SNAP25 and BoNT/A-LC as a model to design SNAP25-derived pseudosubstrate inhibitors (SNAPIs) that prevent presentation of the scissile bond to the active site, we introduced multiple His residues to replace Ala-Asn-Gln-Arg (residues 195-198) at the substrate cleavage site, with the intent to identify possible side-chain interactions with the active site Zn. We also introduced multiple Gly residues between the P1-P1' residues to explore the spatial tolerance within the active-site cleft. Using a FRET substrate YsCsY, we compared a series of SNAPIs for inhibition of BoNT/A-LC. Among the SNAPIs tested, several known cleavage-resistant, single-point mutants of SNAP25 were poor inhibitors, with most of the mutants losing binding affinity. Replacement with His at the active site did not improve inhibition over wildtype substrate. In contrast, Gly-insertion mutants were not only resistant to cleavage, but also surprisingly showed enhanced affinity for BoNT/A-LC. Two of the Gly-insertion mutants exhibited 10-fold lower IC₅₀ values than the wildtype 66-mer SNAP25 peptide. Our findings illustrate a scenario, where the induced fit between enzyme and bound pseudosubstrate fails to produce the strain and distortion required for catalysis to proceed.
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Affiliation(s)
- Mengfei Ho
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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26
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Toth S, Brueggmann EE, Oyler GA, Smith LA, Hines HB, Ahmed SA. Tyrosine phosphorylation of botulinum neurotoxin protease domains. Front Pharmacol 2012; 3:102. [PMID: 22675300 PMCID: PMC3366388 DOI: 10.3389/fphar.2012.00102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 05/07/2012] [Indexed: 01/17/2023] Open
Abstract
Botulinum neurotoxins are most potent of all toxins. Their N-terminal light chain domain (Lc) translocates into peripheral cholinergic neurons to exert its endoproteolytic action leading to muscle paralysis. Therapeutic development against these toxins is a major challenge due to their in vitro and in vivo structural differences. Although three-dimensional structures and reaction mechanisms are very similar, the seven serotypes designated A through G vastly vary in their intracellular catalytic stability. To investigate if protein phosphorylation could account for this difference, we employed Src-catalyzed tyrosine phosphorylation of the Lc of six serotypes namely LcA, LcB, LcC1, LcD, LcE, and LcG. Very little phosphorylation was observed with LcD and LcE but LcA, LcB, and LcG were maximally phosphorylated by Src. Phosphorylation of LcA, LcB, and LcG did not affect their secondary and tertiary structures and thermostability significantly. Phosphorylation of Y250 and Y251 made LcA resistant to autocatalysis and drastically reduced its kcat/Km for catalysis. A tyrosine residue present near the essential cysteine at the C-terminal tail of LcA, LcB, and LcG was readily phosphorylated in vitro. Inclusion of a competitive inhibitor protected Y426 of LcA from phosphorylation, shedding light on the role of the C-terminus in the enzyme’s substrate or product binding.
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Affiliation(s)
- Stephen Toth
- Integrated Toxicology Division, Department of Biochemistry and Cell Biology, United States Army Medical Research Institute of Infectious Diseases Fort Detrick, MD, USA
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27
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Cardellina JH, Roxas-Duncan VI, Montgomery V, Eccard V, Campbell Y, Hu X, Khavrutskii I, Tawa GJ, Wallqvist A, Gloer JB, Phatak NL, Höller U, Soman AG, Joshi BK, Hein SM, Wicklow DT, Smith LA. Fungal bis-Naphthopyrones as Inhibitors of Botulinum Neurotoxin Serotype A. ACS Med Chem Lett 2012; 3:387-91. [PMID: 24900483 DOI: 10.1021/ml200312s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/02/2012] [Indexed: 11/30/2022] Open
Abstract
An in silico screen of the NIH Molecular Library Small Molecule Repository (MLSMR) of ∼350000 compounds and confirmatory bioassays led to identification of chaetochromin A (1) as an inhibitor of botulinum neurotoxin serotype A (BoNT A). Subsequent acquisition and testing of analogues of 1 uncovered two compounds, talaroderxines A (2) and B (3), with improved activity. These are the first fungal metabolites reported to exhibit BoNT/A inhibitory activity.
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Affiliation(s)
- John H. Cardellina
- Division of
Integrated Toxicology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702-5011
| | - Virginia I. Roxas-Duncan
- Division of
Integrated Toxicology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702-5011
| | - Vicki Montgomery
- Division of
Integrated Toxicology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702-5011
| | - Vanessa Eccard
- Division of
Integrated Toxicology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702-5011
| | - Yvette Campbell
- Division of
Integrated Toxicology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702-5011
| | - Xin Hu
- Biotechnology High Performance
Computer Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Materiel Command, Frederick, Maryland 21702
| | - Ilja Khavrutskii
- Biotechnology High Performance
Computer Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Materiel Command, Frederick, Maryland 21702
| | - Gregory J. Tawa
- Biotechnology High Performance
Computer Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Materiel Command, Frederick, Maryland 21702
| | - Anders Wallqvist
- Biotechnology High Performance
Computer Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Materiel Command, Frederick, Maryland 21702
| | - James B. Gloer
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294
| | - Nisarga L. Phatak
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294
| | - Ulrich Höller
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294
| | - Ashish G. Soman
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294
| | - Biren K. Joshi
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294
| | - Sara M. Hein
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294
| | - Donald T. Wicklow
- Bacterial Foodborne Pathogens
and Mycology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604
| | - Leonard A. Smith
- Senior Research Scientist for
Medical Countermeasures Technology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick,
Maryland 21702-5011
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28
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Structure-Based Drug Discovery for Botulinum Neurotoxins. Curr Top Microbiol Immunol 2012; 364:197-218. [DOI: 10.1007/978-3-642-33570-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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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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30
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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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Hale M, Oyler G, Swaminathan S, Ahmed SA. Basic tetrapeptides as potent intracellular inhibitors of type A botulinum neurotoxin protease activity. J Biol Chem 2010; 286:1802-11. [PMID: 20961849 DOI: 10.1074/jbc.m110.146464] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Botulinum neurotoxins (BoNT) are the most potent of all toxins that cause flaccid muscle paralysis leading to death. They are also potential biothreat agents. A systematic investigation of various short peptide inhibitors of the BoNT protease domain with a 17-residue peptide substrate led to arginine-arginine-glycine-cysteine having a basic tetrapeptide structure as the most potent inhibitor. When assayed in the presence of dithiothreitol (DTT), the inhibitory effect was drastically reduced. Replacing the terminal cysteine with one hydrophobic residue eliminated the DTT effect but with two hydrophobic residues made the pentapeptide a poor inhibitor. Replacing the first arginine with cysteine or adding an additional cysteine at the N terminus did not improve inhibition. When assessed using mouse brain lysates, the tetrapeptides also inhibited BoNT/A cleavage of the endogenous SNAP-25. The peptides penetrated the neuronal cell lines, N2A and BE(2)-M17, without adversely affecting metabolic functions as measured by ATP production and P-38 phosphorylation. Biological activity of the peptides persisted within cultured chick motor neurons and rat and mouse cerebellar neurons for more than 40 h and inhibited BoNT/A protease action inside the neurons in a dose- and time-dependent fashion. Our results define a tetrapeptide as the smallest peptide inhibitor in the backdrop of a large substrate protein of 200+ amino acids having multiple interaction regions with its cognate enzyme. The inhibitors should also be valuable candidates for drug development.
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Affiliation(s)
- Martha Hale
- Department Cell Biology and Biochemistry, Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
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32
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Light chain separated from the rest of the type a botulinum neurotoxin molecule is the most catalytically active form. PLoS One 2010; 5:e12872. [PMID: 20877571 PMCID: PMC2943925 DOI: 10.1371/journal.pone.0012872] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 08/20/2010] [Indexed: 11/19/2022] Open
Abstract
Botulinum neurotoxins (BoNT) are the most potent of all toxins. The 50 kDa N-terminal endopeptidase catalytic light chain (LC) of BoNT is located next to its central, putative translocation domain. After binding to the peripheral neurons, the central domain of BoNT helps the LC translocate into cytosol where its proteolytic action on SNARE (soluble NSF attachment protein receptor) proteins blocks exocytosis of acetyl choline leading to muscle paralysis and eventual death. The translocation domain also contains 105 Å -long stretch of ∼100 residues, known as “belt,” that crosses over and wraps around the LC to shield the active site from solvent. It is not known if the LC gets dissociated from the rest of the molecule in the cytosol before catalysis. To investigate the structural identity of the protease, we prepared four variants of type A BoNT (BoNT/A) LC, and compared their catalytic parameters with those of BoNT/A whole toxin. The four variants were LC + translocation domain, a trypsin-nicked LC + translocation domain, LC + belt, and a free LC. Our results showed that Km for a 17-residue SNAP-25 (synaptosomal associated protein of 25 kDa) peptide for these constructs was not very different, but the turnover number (kcat) for the free LC was 6-100-fold higher than those of its four variants. Moreover, none of the four variants of the LC was prone to autocatalysis. Our results clearly demonstrated that in vitro, the LC minus the rest of the molecule is the most catalytically active form. The results may have implication as to the identity of the active, toxic moiety of BoNT/A in vivo.
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Zuniga JE, Hammill JT, Drory O, Nuss JE, Burnett JC, Gussio R, Wipf P, Bavari S, Brunger AT. Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A. PLoS One 2010; 5:e11378. [PMID: 20614028 PMCID: PMC2894858 DOI: 10.1371/journal.pone.0011378] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 06/08/2010] [Indexed: 11/26/2022] Open
Abstract
The botulinum neurotoxin serotype A light chain (BoNT/A LC) protease is the catalytic component responsible for the neuroparalysis that is characteristic of the disease state botulism. Three related peptide-like molecules (PLMs) were designed using previous information from co-crystal structures, synthesized, and assayed for in vitro inhibition against BoNT/A LC. Our results indicate these PLMS are competitive inhibitors of the BoNT/A LC protease and their Ki values are in the nM-range. A co-crystal structure for one of these inhibitors was determined and reveals that the PLM, in accord with the goals of our design strategy, simultaneously involves both ionic interactions via its P1 residue and hydrophobic contacts by means of an aromatic group in the P2′ position. The PLM adopts a helical conformation similar to previously determined co-crystal structures of PLMs, although there are also major differences to these other structures such as contacts with specific BoNT/A LC residues. Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors.
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Affiliation(s)
- Jorge E. Zuniga
- Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, California, United States of America
| | - Jared T. Hammill
- Center for Chemical Methodologies and Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Omri Drory
- Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, California, United States of America
| | - Jonathan E. Nuss
- Division of Bacteriology, Department of Immunology, Target Identification, and Translational Research, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - James C. Burnett
- Target Structure-Based Drug Discovery Group, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Rick Gussio
- Information Technology Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Peter Wipf
- Center for Chemical Methodologies and Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (PW); (ATB)
| | - Sina Bavari
- Division of Bacteriology, Department of Immunology, Target Identification, and Translational Research, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Axel T. Brunger
- Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, California, United States of America
- * E-mail: (PW); (ATB)
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Clostridial neurotoxins: mechanism of SNARE cleavage and outlook on potential substrate specificity reengineering. Toxins (Basel) 2010; 2:665-82. [PMID: 22069605 PMCID: PMC3153214 DOI: 10.3390/toxins2040665] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 03/30/2010] [Accepted: 04/09/2010] [Indexed: 11/17/2022] Open
Abstract
The clostridial neurotoxin family consists of tetanus neurotoxin and seven distinct botulinum neurotoxins which cause the diseases tetanus and botulism. The extreme potency of these toxins primarily relies not only on their ability to specifically enter motoneurons but also on the activity their catalytic domains display inside presynaptic motoneuronal terminals. Subsequent to neurotoxin binding and endocytosis the catalytic domains become translocated across endosomal membranes and proteolyze unique peptide bonds of one of three soluble N-ethylmaleimide-sensitive fusion protein attachment receptors (SNAREs), vesicle associated membrane protein/synaptobrevin, synaptosome associated protein of 25 kDa, or syntaxin. As these substrate proteins are core components of the vesicular membrane fusion apparatus, cleavage of any of the substrate molecules results in the blockade of neurotransmitter release. This review summarizes the present knowledge about the molecular basis of the specific substrate recognition and cleavage mechanism and assesses the feasibility of reengineering catalytic domains to hydrolyze non-substrate members of the three SNARE families in order to expand the therapeutic application of botulinum neurotoxins.
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Li B, Pai R, Cardinale SC, Butler MM, Peet NP, Moir DT, Bavari S, Bowlin TL. Synthesis and biological evaluation of botulinum neurotoxin a protease inhibitors. J Med Chem 2010; 53:2264-76. [PMID: 20155918 DOI: 10.1021/jm901852f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NSC 240898 was previously identified as a botulinum neurotoxin A light chain (BoNT/A LC) endopeptidase inhibitor by screening the National Cancer Institute Open Repository diversity set. Two types of analogues have been synthesized and shown to inhibit BoNT/A LC in a FRET-based enzyme assay, with confirmation in an HPLC-based assay. These two series of compounds have also been evaluated for inhibition of anthrax lethal factor (LF), an unrelated metalloprotease, to examine enzyme specificity of the BoNT/A LC inhibition. The most potent inhibitor against BoNT/A LC in these two series is compound 12 (IC(50) = 2.5 microM, FRET assay), which is 4.4-fold more potent than the lead structure and 11.2-fold more selective for BoNT/A LC versus the anthrax LF metalloproteinase. Structure-activity relationship studies have revealed structural features important to potency and enzyme specificity.
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Affiliation(s)
- Bing Li
- Microbiotix Inc, One Innovation Drive, Worcester, Massachusetts 01605, USA.
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36
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Toth SI, Smith LA, Ahmed SA. Extreme sensitivity of botulinum neurotoxin domains towards mild agitation. J Pharm Sci 2009; 98:3302-11. [PMID: 19226630 DOI: 10.1002/jps.21676] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Botulinum neurotoxins (BoNTs) and their fragments are targets of therapeutic developments and are increasingly used as therapeutic, prophylactic, and research reagents. However, published data on their properties vary widely. In order to gain a better understanding of these variations, we initiated a systematic investigation of the stability parameters of catalytic light chains (Lc) as well as of cell surface binding domains (Hc) of the neurotoxin. When followed by CD spectroscopy, we noticed that the recombinant light chains of serotypes A (LcA), B, D, E, and G rapidly lost their secondary structures by mild stirring. Denaturation of LcA increased with stirring speed and temperature resulting in a catalytically inactive precipitate. Reducing agents or an anaerobic environment were ineffective in the denaturation. Under identical conditions, bovine serum albumin, ovalbumin, carboxypeptidase B, and of thermolysin, a structural and functional analogue of LcA, remained unchanged. Hc domains of serotype A, B, C, E, and F were also denatured by mild stirring. Adding the nonionic detergent Tween-20 to LcA completely prevented the denaturation. We speculate that the BoNT domains undergo surface denaturation due to rapid exposure of hydrophobic residues by mechanical agitation. This study has important implications for handling BoNT proteins used in therapeutic development.
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Affiliation(s)
- Stephen I Toth
- Department Molecular Biology, Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
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Xu T, Zhang L, Wang X, Wei D, Li T. Structure-based substrate screening for an enzyme. BMC Bioinformatics 2009; 10:257. [PMID: 19695105 PMCID: PMC2745390 DOI: 10.1186/1471-2105-10-257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 08/21/2009] [Indexed: 11/10/2022] Open
Abstract
Background Nowadays, more and more novel enzymes can be easily found in the whole enzyme pool with the rapid development of genetic operation. However, experimental work for substrate screening of a new enzyme is laborious, time consuming and costly. On the other hand, many computational methods have been widely used in lead screening of drug design. Seeing that the ligand-target protein system in drug design and the substrate-enzyme system in enzyme applications share the similar molecular recognition mechanism, we aim to fulfill the goal of substrate screening by in silico means in the present study. Results A computer-aided substrate screening (CASS) system which was based on the enzyme structure was designed and employed successfully to help screen substrates of Candida antarctica lipase B (CALB). In this system, restricted molecular docking which was derived from the mechanism of the enzyme was applied to predict the energetically favorable poses of substrate-enzyme complexes. Thereafter, substrate conformation, distance between the oxygen atom of the alcohol part of the ester (in some compounds, this oxygen atom was replaced by nitrogen atom of the amine part of acid amine or sulfur atom of the thioester) and the hydrogen atom of imidazole of His224, distance between the carbon atom of the carbonyl group of the compound and the oxygen atom of hydroxyl group of Ser105 were used sequentially as the criteria to screen the binding poses. 223 out of 233 compounds were identified correctly for the enzyme by this screening system. Such high accuracy guaranteed the feasibility and reliability of the CASS system. Conclusion The idea of computer-aided substrate screening is a creative combination of computational skills and enzymology. Although the case studied in this paper is tentative, high accuracy of the CASS system sheds light on the field of computer-aided substrate screening.
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Affiliation(s)
- Tao Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, PR China.
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38
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Brunger AT, Rummel A. Receptor and substrate interactions of clostridial neurotoxins. Toxicon 2009; 54:550-60. [PMID: 19268493 PMCID: PMC2756235 DOI: 10.1016/j.toxicon.2008.12.027] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 12/01/2008] [Accepted: 12/02/2008] [Indexed: 01/27/2023]
Abstract
The high potency of clostridial neurotoxins relies predominantly on their neurospecific binding and specific hydrolysis of SNARE proteins. Their multi-step mode of mechanism can be ascribed to their multi-domain three-dimensional structure. The C-terminal H(CC)-domain interacts subsequently with complex polysialo-gangliosides such as GT1b and a synaptic vesicle protein receptor via two neighbouring binding sites, resulting in highly specific uptake of the neurotoxins at synapses of cholinergic motoneurons. After its translocation the enzymatically active light chain specifically hydrolyses specific SNARE proteins, preventing SNARE complex assembly and thereby blocking exocytosis of neurotransmitter.
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Affiliation(s)
- Axel T Brunger
- The Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science, Stanford University, J.H. Clark Center, E300C, 318 Campus Drive, Stanford, CA 94305, USA.
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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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40
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Zuniga JE, Schmidt JJ, Fenn T, Burnett JC, Araç D, Gussio R, Stafford RG, Badie SS, Bavari S, Brunger AT. A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate. Structure 2008; 16:1588-97. [PMID: 18940613 PMCID: PMC2716802 DOI: 10.1016/j.str.2008.07.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 07/11/2008] [Accepted: 07/13/2008] [Indexed: 01/07/2023]
Abstract
Botulinum neurotoxin serotype A is the most lethal of all known toxins. Here, we report the crystal structure, along with SAR data, of the zinc metalloprotease domain of BoNT/A bound to a potent peptidomimetic inhibitor (K(i)=41 nM) that resembles the local sequence of the SNAP-25 substrate. Surprisingly, the inhibitor adopts a helical conformation around the cleavage site, in contrast to the extended conformation of the native substrate. The backbone of the inhibitor's P1 residue displaces the putative catalytic water molecule and concomitantly interacts with the "proton shuttle" E224. This mechanism of inhibition is aided by residue contacts in the conserved S1' pocket of the substrate binding cleft and by the induction of new hydrophobic pockets, which are not present in the apo form, especially for the P2' residue of the inhibitor. Our inhibitor is specific for BoNT/A as it does not inhibit other BoNT serotypes or thermolysin.
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Affiliation(s)
- Jorge E. Zuniga
- Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, CA 94305, USA
| | - James J. Schmidt
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Timothy Fenn
- Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, CA 94305, USA
| | - James C. Burnett
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702
| | - Demet Araç
- Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, CA 94305, USA
| | - Rick Gussio
- Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21702
| | - Robert G. Stafford
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Shirin S. Badie
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Axel T. Brunger
- Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Stanford University, Stanford, CA 94305, USA,Corresponding author: , Phone number: 650-736-1031, Fax number: 650-736-1961
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Substrate binding mode and its implication on drug design for botulinum neurotoxin A. PLoS Pathog 2008; 4:e1000165. [PMID: 18818739 PMCID: PMC2533696 DOI: 10.1371/journal.ppat.1000165] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 08/28/2008] [Indexed: 11/19/2022] Open
Abstract
The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC) has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A), cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25). An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide (197)QRATKM(202) and its variant (197)RRATKM(202) to 1.5 A and 1.6 A, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5' sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197) chelate the zinc ion and replace the nucleophilic water. The P1'-Arg198, occupies the S1' site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2' subsite is formed by Arg363, Asn368 and Asp370, while S3' subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4'-Lys201 makes hydrogen bond with Gln162. P5'-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin.
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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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