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Altei WF, Picchi DG, Abissi BM, Giesel GM, Flausino O, Reboud-Ravaux M, Verli H, Crusca E, Silveira ER, Cilli EM, Bolzani VS. Jatrophidin I, a cyclic peptide from Brazilian Jatropha curcas L.: isolation, characterization, conformational studies and biological activity. PHYTOCHEMISTRY 2014; 107:91-96. [PMID: 25200101 DOI: 10.1016/j.phytochem.2014.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/09/2014] [Accepted: 08/07/2014] [Indexed: 06/03/2023]
Abstract
A cyclic peptide, jatrophidin I, was isolated from the latex of Jatropha curcas L. Its structure was elucidated by extensive 2D NMR spectroscopic analysis, with additional conformational studies performed using Molecular Dynamics/Simulated Annealing (MD/SA). Jatrophidin I had moderate protease inhibition activity when compared with pepstatin A; however, the peptide was inactive in antimalarial, cytotoxic and antioxidant assays.
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Affiliation(s)
- Wanessa F Altei
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil
| | - Douglas G Picchi
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil
| | - Barbara M Abissi
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil
| | - Guilherme M Giesel
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
| | - Otavio Flausino
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil
| | - Michèle Reboud-Ravaux
- Enzymologie Moléculaire et Fonctionnelle, UR4, UPMC, Sorbonne Universités, 7 Quai St Bernard, 75252 Paris Cedex 05, France
| | - Hugo Verli
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av Ipiranga 2752, Porto Alegre 90610-000, RS, Brazil
| | - Edson Crusca
- Departamento de Bioquímica e Biotecnologia, Instituto de Química Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil
| | - Edilberto R Silveira
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE 60.430-270, Brazil
| | - Eduardo M Cilli
- Departamento de Bioquímica e Biotecnologia, Instituto de Química Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil
| | - Vanderlan S Bolzani
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Julio de Mesquita Filho', CP 355, 14801-970 Araraquara, SP, Brazil.
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Fuchs JE, von Grafenstein S, Huber RG, Kramer C, Liedl KR. Substrate-driven mapping of the degradome by comparison of sequence logos. PLoS Comput Biol 2013; 9:e1003353. [PMID: 24244149 PMCID: PMC3828135 DOI: 10.1371/journal.pcbi.1003353] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/05/2013] [Indexed: 12/27/2022] Open
Abstract
Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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Brylinski M, Skolnick J. FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol 2009; 5:e1000405. [PMID: 19503616 PMCID: PMC2685473 DOI: 10.1371/journal.pcbi.1000405] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 05/05/2009] [Indexed: 11/19/2022] Open
Abstract
Ligand virtual screening is a widely used tool to assist in new pharmaceutical
discovery. In practice, virtual screening approaches have a number of
limitations, and the development of new methodologies is required. Previously,
we showed that remotely related proteins identified by threading often share a
common binding site occupied by chemically similar ligands. Here, we demonstrate
that across an evolutionarily related, but distant family of proteins, the
ligands that bind to the common binding site contain a set of strongly conserved
anchor functional groups as well as a variable region that accounts for their
binding specificity. Furthermore, the sequence and structure conservation of
residues contacting the anchor functional groups is significantly higher than
those contacting ligand variable regions. Exploiting these insights, we
developed FINDSITELHM that employs structural information extracted
from weakly related proteins to perform rapid ligand docking by homology
modeling. In large scale benchmarking, using the predicted anchor-binding mode
and the crystal structure of the receptor, FINDSITELHM outperforms
classical docking approaches with an average ligand RMSD from native of
∼2.5 Å. For weakly homologous receptor protein models, using
FINDSITELHM, the fraction of recovered binding residues and
specific contacts is 0.66 (0.55) and 0.49 (0.38) for highly confident (all)
targets, respectively. Finally, in virtual screening for HIV-1 protease
inhibitors, using similarity to the ligand anchor region yields significantly
improved enrichment factors. Thus, the rather accurate, computationally
inexpensive FINDSITELHM algorithm should be a useful approach to
assist in the discovery of novel biopharmaceuticals. As an integral part of drug development, high-throughput virtual screening is a
widely used tool that could in principle significantly reduce the cost and time
to discovery of new pharmaceuticals. In practice, virtual screening algorithms
suffer from a number of limitations. The high sensitivity of all-atom ligand
docking approaches to the quality of the target receptor structure restricts the
selection of drug targets to those for which high-quality X-ray structures are
available. Furthermore, the predicted binding affinity is typically strongly
correlated with the molecular weight of the ligand, independent of whether or
not it really binds. To address these significant problems, we developed
FINDSITELHM, a novel threading-based approach that employs
structural information extracted from weakly related proteins to perform rapid
ligand docking and ranking that is very much in the spirit of homology modeling
of protein structures. Particularly for low-quality modeled receptor structures,
FINDSITELHM outperforms classical all-atom ligand docking
approaches in terms of the accuracy of ligand binding pose prediction and
requires considerably less CPU time. As an attractive alternative to classical
molecular docking, FINDSITELHM offers the possibility of rapid
structure-based virtual screening at the proteome level to improve and speed up
the discovery of new biopharmaceuticals.
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Affiliation(s)
- Michal Brylinski
- Center for the Study of Systems Biology, School of Biology, Georgia
Institute of Technology, Atlanta, Georgia, United States of America
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia
Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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