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Colombo É, Désilets A, Hassanzadeh M, Lemieux G, Marois I, Cliche D, Delbrouck JA, Murza A, Jean F, Marsault E, Richter MV, Leduc R, Boudreault PL. Optimization of Ketobenzothiazole-Based Type II Transmembrane Serine Protease Inhibitors to Block H1N1 Influenza Virus Replication. ChemMedChem 2024; 19:e202300458. [PMID: 37864572 DOI: 10.1002/cmdc.202300458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Human influenza viruses cause acute respiratory symptoms that can lead to death. Due to the emergence of antiviral drug-resistant strains, there is an urgent requirement for novel antiviral agents and innovative therapeutic strategies. Using the peptidomimetic ketobenzothiazole protease inhibitor RQAR-Kbt (IN-1, aka N-0100) as a starting point, we report how substituting P2 and P4 positions with natural and unnatural amino acids can modulate the inhibition potency toward matriptase, a prototypical type II transmembrane serine protease (TTSP) that acts as a priming protease for influenza viruses. We also introduced modifications of the peptidomimetics N-terminal groups, leading to significant improvements (from μM to nM, 60 times more potent than IN-1) in their ability to inhibit the replication of influenza H1N1 virus in the Calu-3 cell line derived from human lungs. The selectivity towards other proteases has been evaluated and explained using molecular modeling with a crystal structure recently obtained by our group. By targeting host cell TTSPs as a therapeutic approach, it may be possible to overcome the high mutational rate of influenza viruses and consequently prevent potential drug resistance.
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Affiliation(s)
- Éloïc Colombo
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Antoine Désilets
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Malihe Hassanzadeh
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Gabriel Lemieux
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Isabelle Marois
- Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4 Québec, Canada
- Current address: Department of Biology, Faculty of Sciences, Université de Sherbrooke, Sherbrooke, J1K 2R1 Québec, Canada
| | - Dominic Cliche
- Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4 Québec, Canada
| | - Julien A Delbrouck
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Current address: Xenon Pharmaceuticals Inc., Burnaby, V5G 4W8, British Columbia, Canada
| | - Alexandre Murza
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - François Jean
- Department of Microbiology and Immunology, Faculty of Science, Life Sciences Institute, University of British Columbia, V6T 1Z3, British Columbia, Canada
| | - Eric Marsault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Martin V Richter
- Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4 Québec, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
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2
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McCabe MC, Gejji V, Barnebey A, Siuzdak G, Hoang LT, Pham T, Larson KY, Saviola AJ, Yannone SM, Hansen KC. From volcanoes to the bench: Advantages of novel hyperthermoacidic archaeal proteases for proteomics workflows. J Proteomics 2023; 289:104992. [PMID: 37634627 DOI: 10.1016/j.jprot.2023.104992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
Here we introduce hyperthermoacidic archaeal proteases (HTA-Proteases©) isolated from organisms that thrive in nearly boiling acidic volcanic springs and investigate their use for bottom-up proteomic experiments. We find that HTA-Proteases have novel cleavage specificities, show no autolysis, function in dilute formic acid, and store at ambient temperature for years. HTA-Proteases function optimally at 70-90 °C and pH of 2-4 with rapid digestion kinetics. The extreme HTA-Protease reaction conditions actively denature sample proteins, obviate the use of chaotropes, are largely independent of reduction and alkylation, and allow for a one-step/five-minute sample preparation protocol without sample manipulation, dilution, or additional cleanup. We find that brief one-step HTA-Protease protocols significantly increase proteome and protein sequence coverage with datasets orthogonal to trypsin. Importantly, HTA-Protease digests markedly increase coverage and identifications for ribonucleoproteins, histones, and mitochondrial membrane proteins as compared to tryptic digests alone. In addition to increased coverage in these classes, HTA-Proteases and simplified one-step protocols are expected to reduce technical variability and advance the fields of clinical and high-throughput proteomics. This work reveals significant utility of heretofore unavailable HTA-Proteases for proteomic workflows. We discuss some of the potential for these remarkable enzymes to empower new proteomics methods, approaches, and biological insights. SIGNIFICANCE: Here we introduce new capabilities for bottom-up proteomics applications with hyperthermoacidic archaeal proteases (HTA-Proteases©). HTA-Proteases have novel cleavage specificity, require no chaotropes, and allow simple one-step/five-minute sample preparations that promise to reduce variability between samples and laboratories. HTA-Proteases generate unique sets of observable peptides that are non-overlapping with tryptic peptides and significantly increase sequence coverage and available peptide targets relative to trypsin alone. HTA-Proteases show some bias for the detection and coverage of nucleic acid-binding proteins and membrane proteins relative to trypsin. These new ultra-stable enzymes function optimally in nearly boiling acidic conditions, show no autolysis, and do not require aliquoting as they are stable for years at ambient temperatures. Used independently or in conjunction with tryptic digests, HTA-Proteases offer increased proteome coverage, unique peptide targets, and brief one-step protocols amenable to automation, rapid turnaround, and high-throughput approaches.
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Affiliation(s)
- Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Varun Gejji
- Cinder Biological, Inc., 1933 Davis Street, STE 208, San Leandro, CA 94577, USA
| | - Adam Barnebey
- Cinder Biological, Inc., 1933 Davis Street, STE 208, San Leandro, CA 94577, USA
| | - Gary Siuzdak
- Departments of Chemistry, Molecular, and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Linh Truc Hoang
- Departments of Chemistry, Molecular, and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Truc Pham
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Keira Y Larson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Steven M Yannone
- Cinder Biological, Inc., 1933 Davis Street, STE 208, San Leandro, CA 94577, USA.
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA.
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3
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Matveev EV, Safronov VV, Ponomarev GV, Kazanov MD. Predicting Structural Susceptibility of Proteins to Proteolytic Processing. Int J Mol Sci 2023; 24:10761. [PMID: 37445939 DOI: 10.3390/ijms241310761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The importance of 3D protein structure in proteolytic processing is well known. However, despite the plethora of existing methods for predicting proteolytic sites, only a few of them utilize the structural features of potential substrates as predictors. Moreover, to our knowledge, there is currently no method available for predicting the structural susceptibility of protein regions to proteolysis. We developed such a method using data from CutDB, a database that contains experimentally verified proteolytic events. For prediction, we utilized structural features that have been shown to influence proteolysis in earlier studies, such as solvent accessibility, secondary structure, and temperature factor. Additionally, we introduced new structural features, including length of protruded loops and flexibility of protein termini. To maximize the prediction quality of the method, we carefully curated the training set, selected an appropriate machine learning method, and sampled negative examples to determine the optimal positive-to-negative class size ratio. We demonstrated that combining our method with models of protease primary specificity can outperform existing bioinformatics methods for the prediction of proteolytic sites. We also discussed the possibility of utilizing this method for bioinformatics prediction of other post-translational modifications.
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Affiliation(s)
- Evgenii V Matveev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117998, Russia
| | - Vyacheslav V Safronov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Gennady V Ponomarev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Marat D Kazanov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117998, Russia
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
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Sun Y, Zhao B, Wang Y, Chen Z, Zhang H, Qu L, Zhao Y, Song J. Optimization of potential non-covalent inhibitors for the SARS-CoV-2 main protease inspected by a descriptor of the subpocket occupancy. Phys Chem Chem Phys 2022; 24:29940-29951. [PMID: 36468652 DOI: 10.1039/d2cp03681a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The main protease is regarded as an essential drug target for treating Coronavirus Disease 2019. In the present study, 13 marketed drugs were investigated to explore the possible binding mechanism, utilizing molecular docking, molecular dynamics simulation, and MM-PB(GB)SA binding energy calculations. Our results suggest that fusidic acid, polydatin, SEN-1269, AZD6482, and UNC-2327 have high binding affinities of more than 23 kcal mol-1. A descriptor was defined for the energetic occupancy of the subpocket, and it was found that S4 had a low occupancy of less than 10% on average. The molecular optimization of ADZ6482 via reinforcement learning algorithms was carried out to screen out three lead compounds, in which slight structural changes give more considerable binding energies and an occupancy of the S4 subpocket of up to 43%. The energetic occupancy could be a useful descriptor for evaluating the local binding affinity for drug design.
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Affiliation(s)
- Yujia Sun
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Bodi Zhao
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Yuqi Wang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Zitong Chen
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Huaiyu Zhang
- Institute of Computational Quantum Chemistry, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Lingbo Qu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno - Engineering, Henan University, Kaifeng, Henan, 475000, P. R. China
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
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5
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Ochoa R, Cossio P. PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules 2021; 26:molecules26061664. [PMID: 33809815 PMCID: PMC8002403 DOI: 10.3390/molecules26061664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 11/27/2022] Open
Abstract
Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin 050010, Colombia;
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin 050010, Colombia;
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60348 Frankfurt am Main, Germany
- Correspondence:
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
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7
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Quantitative profiling of protease specificity. PLoS Comput Biol 2021; 17:e1008101. [PMID: 33617527 PMCID: PMC7932537 DOI: 10.1371/journal.pcbi.1008101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/04/2021] [Accepted: 01/28/2021] [Indexed: 12/30/2022] Open
Abstract
Proteases are an important class of enzymes, whose activity is central to many physiologic and pathologic processes. Detailed knowledge of protease specificity is key to understanding their function. Although many methods have been developed to profile specificities of proteases, few have the diversity and quantitative grasp necessary to fully define specificity of a protease, both in terms of substrate numbers and their catalytic efficiencies. We have developed a concept of “selectome”; the set of substrate amino acid sequences that uniquely represent the specificity of a protease. We applied it to two closely related members of the Matrixin family–MMP-2 and MMP-9 by using substrate phage display coupled with Next Generation Sequencing and information theory-based data analysis. We have also derived a quantitative measure of substrate specificity, which accounts for both the number of substrates and their relative catalytic efficiencies. Using these advances greatly facilitates elucidation of substrate selectivity between closely related members of a protease family. The study also provides insight into the degree to which the catalytic cleft defines substrate recognition, thus providing basis for overcoming two of the major challenges in the field of proteolysis: 1) development of highly selective activity probes for studying proteases with overlapping specificities, and 2) distinguishing targeted proteolysis from bystander proteolytic events. Proteases and proteolysis are intimately involved in virtually all biological processes from embryonic development to programmed cell death and cellular protein recycling. As the only irreversible posttranslational modification, proteolysis represents a committed step in regulation of biological networks and pathways. Imbalance of proteolytic activity has catastrophic implications and is the basis of many genetic disorders as well as a multitude of pathological states of varying etiologies. To understand protease function, one must gain insight into the repertoires of substrates targeted by these enzymes. As many proteases recognize a wide variety of sequences in proteins, it is a challenge to establish if a particular cleavage represents a targeted or a bystander proteolytic event. In addition, since many proteases have overlapping specificities, especially among closely related members of the same gene families, it is a challenge to develop highly selective tools for studying or inhibition of these enzymes. In this work, we used two closely related proteases (MMP-2 and 9) as a model system for development of an information theory-based approach to quantification of substrate specificity and demonstrated its potential for distinguishing between the target and bystander proteolytic events as well as for uncovering selectivity between closely related proteases.
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Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM. An automated protocol for modelling peptide substrates to proteases. BMC Bioinformatics 2020; 21:586. [PMID: 33375946 PMCID: PMC7771086 DOI: 10.1186/s12859-020-03931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/09/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition. RESULTS As an application, we modelled a subset of protease-peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease-specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease's substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. CONCLUSION Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease-peptide complexes.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, 050010, Medellín, Colombia.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Mikhail Magnitov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia, 141701
| | - Roman A Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, 050010, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Öhlknecht C, Petrov D, Engele P, Kröß C, Sprenger B, Fischer A, Lingg N, Schneider R, Oostenbrink C. Enhancing the promiscuity of a member of the Caspase protease family by rational design. Proteins 2020; 88:1303-1318. [PMID: 32432825 PMCID: PMC7497161 DOI: 10.1002/prot.25950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/19/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
The N-terminal cleavage of fusion tags to restore the native N-terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in-silico to yield enhanced promiscuity toward different N-terminal amino acids. Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease. These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations. The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results. Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids. We believe that the created mutants constitute an important step toward generalized procedures to restore original N-termini of recombinant fusion proteins.
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Affiliation(s)
- Christoph Öhlknecht
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Drazen Petrov
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
| | - Petra Engele
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Christina Kröß
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Bernhard Sprenger
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | | | - Nico Lingg
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Rainer Schneider
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
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10
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Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J. Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Brief Bioinform 2019; 20:2150-2166. [PMID: 30184176 PMCID: PMC6954447 DOI: 10.1093/bib/bby077] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 01/06/2023] Open
Abstract
The roles of proteolytic cleavage have been intensively investigated and discussed during the past two decades. This irreversible chemical process has been frequently reported to influence a number of crucial biological processes (BPs), such as cell cycle, protein regulation and inflammation. A number of advanced studies have been published aiming at deciphering the mechanisms of proteolytic cleavage. Given its significance and the large number of functionally enriched substrates targeted by specific proteases, many computational approaches have been established for accurate prediction of protease-specific substrates and their cleavage sites. Consequently, there is an urgent need to systematically assess the state-of-the-art computational approaches for protease-specific cleavage site prediction to further advance the existing methodologies and to improve the prediction performance. With this goal in mind, in this article, we carefully evaluated a total of 19 computational methods (including 8 scoring function-based methods and 11 machine learning-based methods) in terms of their underlying algorithm, calculated features, performance evaluation and software usability. Then, extensive independent tests were performed to assess the robustness and scalability of the reviewed methods using our carefully prepared independent test data sets with 3641 cleavage sites (specific to 10 proteases). The comparative experimental results demonstrate that PROSPERous is the most accurate generic method for predicting eight protease-specific cleavage sites, while GPS-CCD and LabCaS outperformed other predictors for calpain-specific cleavage sites. Based on our review, we then outlined some potential ways to improve the prediction performance and ease the computational burden by applying ensemble learning, deep learning, positive unlabeled learning and parallel and distributed computing techniques. We anticipate that our study will serve as a practical and useful guide for interested readers to further advance next-generation bioinformatics tools for protease-specific cleavage site prediction.
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Affiliation(s)
- Fuyi Li
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Yanan Wang
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Department of Biology, Institute of Molecular Systems Biology,ETH Zürich, Zürich 8093, Switzerland
| | - Tatiana T Marquez-Lago
- Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - André Leier
- Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Neil D Rawlings
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gholamreza Haffari
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Jerico Revote
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, USA
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Robert N Pike
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - A Ian Smith
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Trevor Lithgow
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Roger J Daly
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - James C Whisstock
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
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11
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Qi E, Wang D, Li Y, Li G, Su Z. Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites. Biochem Biophys Res Commun 2019; 519:714-720. [PMID: 31543345 DOI: 10.1016/j.bbrc.2019.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 11/17/2022]
Abstract
Proteases play critical roles in a wide variety of fundamental biological functions, and numerous protease inhibitors have been developed to treat various diseases including cancer. A wide range of experimental and computational methods have been developed to investigate the specificity and catalytic mechanisms of proteases. However, these methods only focused on the preferences of a single position around a cleavage site in a substrate, rarely on the compositionality of the subsites. We present new methods to quantify the specificity of proteases by considering the combinatorial patterns of amino acid residuals of cleavage sites in substrates. By incorporating the preference at positions, we modeled three types of favorable combinations of residues in cleavage sites. Moreover, by constructing a relationship weight matrix of residues between two positions, we can easily identify unfavorable combinations of residues at the positions. Applying these methods to a set of known cleavage sites of proteases, we revealed numerous favorable and unfavorable residues in cooperative positions in the protease cleavage sites. The results can help understand the specificity and catalytic mechanisms of proteases. To our knowledge, this is the first study that quantifies unfavorable combinations of amino acids between two sites. Furthermore, this method is not limited to the study of proteases and cleavage sites, and can be generalized to uncover the relationships of residues at meaningful sites in other proteins.
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Affiliation(s)
- Enfeng Qi
- School of Mathematics, Shandong University, Jinan, 250100, China; School of Mathematics and Statistics, Guangxi Normal University, Guilin, 541000, China
| | - Dongyu Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Yang Li
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, 28223, USA.
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12
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Kraml J, Kamenik AS, Waibl F, Schauperl M, Liedl KR. Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces. J Chem Theory Comput 2019; 15:5872-5882. [PMID: 31589427 PMCID: PMC7032847 DOI: 10.1021/acs.jctc.9b00742] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 12/27/2022]
Abstract
Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In substrate binding, but also in structure-based drug design, the thermodynamic properties of water molecules surrounding a given protein are of high interest. One of the main algorithms devised in recent years to quantify thermodynamic properties of water is the grid inhomogeneous solvation theory (GIST), which calculates these features on a grid surrounding the protein. Despite the inherent advantages of GIST, the computational demand is a major drawback, as calculations for larger systems can take days or even weeks. Here, we present a GPU accelerated version of the GIST algorithm, which facilitates efficient estimates of solvation free energy even of large biomolecular interfaces. Furthermore, we show that GIST can be used as a reliable tool to evaluate protein surface hydrophobicity. We apply the approach on a set of nine different proteases calculating localized solvation free energies on the surface of the binding interfaces as a measure of their hydrophobicity. We find a compelling agreement with the hydrophobicity of their substrates, i.e., peptides, binding into the binding cleft, and thus our approach provides a reliable description of hydrophobicity characteristics of these biological interfaces.
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Affiliation(s)
- Johannes Kraml
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| | - Anna S. Kamenik
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| | - Franz Waibl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| | - Michael Schauperl
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92039-0736, United States
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
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13
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Majewski M, Ruiz-Carmona S, Barril X. An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Commun Chem 2019. [DOI: 10.1038/s42004-019-0205-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. However, structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, it entails an entropic penalty that counters complex formation. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Since hydrogen bonds have been described as essential for structural stability, here we investigate 469 such interactions across two diverse structure sets, comprising of 79 drug-like and 27 fragment ligands, respectively. Completely constricted protein-ligand complexes are rare and may fulfill a functional role. Most complexes balance order and disorder by combining a single anchoring point with looser regions. 25% do not contain any robust hydrogen bond and may form loose structures. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
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14
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Fedonin GG, Eroshkin A, Cieplak P, Matveev EV, Ponomarev GV, Gelfand MS, Ratnikov BI, Kazanov MD. Predictive models of protease specificity based on quantitative protease-activity profiling data. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140253. [PMID: 31330204 DOI: 10.1016/j.bbapap.2019.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/09/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
Bioinformatics-based prediction of protease substrates can help to elucidate regulatory proteolytic pathways that control a broad range of biological processes such as apoptosis and blood coagulation. The majority of published predictive models are position weight matrices (PWM) reflecting specificity of proteases toward target sequence. These models are typically derived from experimental data on positions of hydrolyzed peptide bonds and show a reasonable predictive power. New emerging techniques that not only register the cleavage position but also measure catalytic efficiency of proteolysis are expected to improve the quality of predictions or at least substantially reduce the number of tested substrates required for confident predictions. The main goal of this study was to develop new prediction models based on such data and to estimate the performance of the constructed models. We used data on catalytic efficiency of proteolysis measured for eight major human matrix metalloproteinases to construct predictive models of protease specificity using a variety of regression analysis techniques. The obtained results suggest that efficiency-based (quantitative) models show a comparable performance with conventional PWM-based algorithms, while less training data are required. The derived list of candidate cleavage sites in human secreted proteins may serve as a starting point for experimental analysis.
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Affiliation(s)
- Gennady G Fedonin
- Central Research Institute of Epidemiology, Moscow 111123, Russia; A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Alexey Eroshkin
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Piotr Cieplak
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Gennady V Ponomarev
- A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Moscow 121205, Russia; National Research University Higher School of Economics, Moscow 101000, Russia
| | - Boris I Ratnikov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Marat D Kazanov
- A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117997, Russia.
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15
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Kahler U, Fuchs JE, Goettig P, Liedl KR. An unexpected switch in peptide binding mode: from simulation to substrate specificity. J Biomol Struct Dyn 2018; 36:4072-4084. [PMID: 29210603 PMCID: PMC6334781 DOI: 10.1080/07391102.2017.1407674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/15/2017] [Indexed: 12/12/2022]
Abstract
A ten microsecond molecular dynamics simulation of a kallikrein-related peptidase 7 peptide complex revealed an unexpected change in binding mode. After more than two microseconds unrestrained sampling we observe a spontaneous transition of the binding pose including a 180° rotation around the P1 residue. Subsequently, the substrate peptide occupies the prime side region rather than the cognate non-prime side in a stable conformation. We characterize the unexpected binding mode in terms of contacts, solvent-accessible surface area, molecular interactions and energetic properties. We compare the new pose to inhibitor-bound structures of kallikreins with occupied prime side and find that a similar orientation is adopted. Finally, we apply in silico mutagenesis based on the alternative peptide binding position to explore the prime side specificity of kallikrein-related peptidase 7 and compare it to available experimental data. Our study provides the first microsecond time scale simulation data on a kallikrein protease and shows previously unexplored prime side interactions. Therefore, we expect our study to advance the rational design of inhibitors targeting kallikrein-related peptidase 7, an emerging drug target involved in several skin diseases as well as cancer.
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Affiliation(s)
- Ursula Kahler
- Faculty of Chemistry and Pharmacy, Institute of General, Inorganic and Theoretical Chemistry, University Innsbruck, Innrain 82, InnsbruckA-6020, Austria
| | - Julian E. Fuchs
- Faculty of Chemistry and Pharmacy, Institute of General, Inorganic and Theoretical Chemistry, University Innsbruck, Innrain 82, InnsbruckA-6020, Austria
| | - Peter Goettig
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, SalzburgA-5020, Austria
| | - Klaus R. Liedl
- Faculty of Chemistry and Pharmacy, Institute of General, Inorganic and Theoretical Chemistry, University Innsbruck, Innrain 82, InnsbruckA-6020, Austria
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16
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Ding B, Martin DW, Rampello AJ, Glynn SE. Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease. Biochemistry 2018; 57:4225-4235. [PMID: 29932645 DOI: 10.1021/acs.biochem.8b00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. Identifying how AFG3L2 selects substrates from the diverse complement of matrix-localized proteins is essential for understanding mitochondrial protein biogenesis and quality control. Here, we create solubilized forms of AFG3L2 to examine the enzyme's substrate specificity mechanisms. We show that conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form. Moreover, these residues can act as a degron, delivering diverse model proteins to AFG3L2 for degradation. By determining the sequence of degradation products from multiple substrates using mass spectrometry, we construct a peptidase specificity profile that displays constrained product lengths and is dominated by the identity of the residue at the P1' position, with a strong preference for hydrophobic and small polar residues. This specificity profile is validated by examining the cleavage of both fluorogenic reporter peptides and full polypeptide substrates bearing different P1' residues. Together, these results demonstrate that AFG3L2 contains multiple modes of specificity, discriminating between potential substrates by recognizing accessible degron sequences and performing peptide bond cleavage at preferred patterns of residues within the compartmental chamber.
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17
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Waldner BJ, Kraml J, Kahler U, Spinn A, Schauperl M, Podewitz M, Fuchs JE, Cruciani G, Liedl KR. Electrostatic recognition in substrate binding to serine proteases. J Mol Recognit 2018; 31:e2727. [PMID: 29785722 PMCID: PMC6175425 DOI: 10.1002/jmr.2727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022]
Abstract
Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes. Thus, we are able to directly link protease structures to their electrostatic substrate preferences. Additionally, we present a new metric that measures similarities in substrate preferences focusing only on electrostatics. It efficiently compares these electrostatic substrate preferences between different proteases. This new metric can be interpreted as the electrostatic part of our previously developed substrate similarity metric. Consequently, we suggest, that substrate recognition in terms of electrostatics and shape complementarity are rather orthogonal aspects of substrate recognition. This is in line with a 2‐step mechanism of protein‐protein recognition suggested in the literature.
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Affiliation(s)
- Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Ursula Kahler
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Alexander Spinn
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Gabriele Cruciani
- Laboratory of Chemometrics, Department of Chemistry, University of Perugia, Perugia, Italy
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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18
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Packer MS, Rees HA, Liu DR. Phage-assisted continuous evolution of proteases with altered substrate specificity. Nat Commun 2017; 8:956. [PMID: 29038472 PMCID: PMC5643515 DOI: 10.1038/s41467-017-01055-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/14/2017] [Indexed: 01/15/2023] Open
Abstract
Here we perform phage-assisted continuous evolution (PACE) of TEV protease, which canonically cleaves ENLYFQS, to cleave a very different target sequence, HPLVGHM, that is present in human IL-23. A protease emerging from ∼2500 generations of PACE contains 20 non-silent mutations, cleaves human IL-23 at the target peptide bond, and when pre-mixed with IL-23 in primary cultures of murine splenocytes inhibits IL-23-mediated immune signaling. We characterize the substrate specificity of this evolved enzyme, revealing shifted and broadened specificity changes at the six positions in which the target amino acid sequence differed. Mutational dissection and additional protease specificity profiling reveal the molecular basis of some of these changes. This work establishes the capability of changing the substrate specificity of a protease at many positions in a practical time scale and provides a foundation for the development of custom proteases that catalytically alter or destroy target proteins for biotechnological and therapeutic applications.Proteases are promising therapeutics to treat diseases such as hemophilia which are due to endogenous protease deficiency. Here the authors use phage-assisted continuous evolution to evolve a variant TEV protease with altered target peptide sequence specificities.
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Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Graduate Program in Biophysics Program, Harvard University, 240 Longwood Avenue, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA. .,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
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19
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Qi E, Wang D, Gao B, Li Y, Li G. Block-based characterization of protease specificity from substrate sequence profile. BMC Bioinformatics 2017; 18:438. [PMID: 28974219 PMCID: PMC5627433 DOI: 10.1186/s12859-017-1851-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/26/2017] [Indexed: 01/12/2023] Open
Abstract
Background The mechanism of action of proteases has been widely studied based on substrate specificity. Prior research has been focused on the amino acids at a single amino acid site, but rarely on combinations of amino acids around the cleavage bond. Results We propose a novel block-based approach to reveal the potential combinations of amino acids which may regulate the action of proteases. Using the entropies of eight blocks centered at a cleavage bond, we created a distance matrix for 61 proteases to compare their specificities. After quantitative analysis, we discovered a number of prominent blocks, each of which consists of successive amino acids near a cleavage bond, intuitively characterizing the site cooperation of the substrate sequences. Conclusion This approach will help in the discovery of specific substrate sequences which may bridge between proteases and cleavage substrate as more substrate information becomes available. Electronic supplementary material The online version of this article (10.1186/s12859-017-1851-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enfeng Qi
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Dongyu Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Bo Gao
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Yang Li
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
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20
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Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB. Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites. Sci Rep 2017; 7:5755. [PMID: 28720874 PMCID: PMC5515926 DOI: 10.1038/s41598-017-06219-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/08/2017] [Indexed: 11/24/2022] Open
Abstract
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.
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Affiliation(s)
- Yanan Wang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jiangning Song
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana T Marquez-Lago
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - André Leier
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Chen Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
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21
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Fuchs JE, Schilling O, Liedl KR. Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. Curr Protein Pept Sci 2017; 18:905-913. [PMID: 27455965 PMCID: PMC5898033 DOI: 10.2174/1389203717666160724211231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/30/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. METHOD Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. RESULTS AND CONCLUSION We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
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Affiliation(s)
- Julian E. Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, D-79104 Freiburg, Germany and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104Freiburg, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020Innsbruck, Austria
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22
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Zhou J, Huang X, Zhang Z, Song P, Li Y. Trypsin-catalyzed multicomponent reaction: A novel and efficient one-pot synthesis of thiazole-2-imine derivatives. J Biotechnol 2016; 241:14-21. [PMID: 27825826 DOI: 10.1016/j.jbiotec.2016.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/25/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022]
Abstract
The first Trypsin from porcine pancreas catalyzed a novel one-pot three-component reaction of α-bromoketone, primary alkylamines, and phenylisothiocyanate for the synthesis of thiazole-imine derivatives with high yields (up to 98%) in a short time under mild conditions. The results revealed that Trypsin exhibited excellent catalytic activity and great tolerance for broad substrates. This Trypsin-catalyzed three component convergent method provides a novel strategy for the synthesis of thiazole-2-imine derivatives and expands the promiscuous functions of enzymes in organic synthesis.
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Affiliation(s)
- Junbin Zhou
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Xingtian Huang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Zhuan Zhang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Ping Song
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Yiqun Li
- Department of Chemistry, Jinan University, Guangzhou 510632, China.
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23
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Schneider P, Röthlisberger M, Reker D, Schneider G. Spotting and designing promiscuous ligands for drug discovery. Chem Commun (Camb) 2016; 52:1135-8. [PMID: 26602698 DOI: 10.1039/c5cc07506h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The promiscuous binding behavior of bioactive compounds forms a mechanistic basis for understanding polypharmacological drug action. We present the development and prospective application of a computational tool for identifying potential promiscuous drug-like ligands. In combination with computational target prediction methods, the approach provides a working concept for rationally designing such molecular structures. We could confirm the multi-target binding of a de novo generated compound in a proof-of-concept study relying on the new method.
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Affiliation(s)
- P Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland. and inSili.com LLC, Segantinisteig 3, 8049 Zürich, Switzerland.
| | - M Röthlisberger
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
| | - D Reker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
| | - G Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
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24
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Ozdemir Isik G, Ozer AN. Prediction of substrate specificity in NS3/4A serine protease by biased sequence search threading. J Biomol Struct Dyn 2016; 35:1102-1114. [DOI: 10.1080/07391102.2016.1171801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Gonca Ozdemir Isik
- Department of Bioengineering, Marmara University , Goztepe, Kadikoy, 34722 Istanbul, Turkey
| | - A. Nevra Ozer
- Department of Bioengineering, Marmara University , Goztepe, Kadikoy, 34722 Istanbul, Turkey
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25
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Waldner B, Fuchs JE, Schauperl M, Kramer C, Liedl KR. Protease Inhibitors in View of Peptide Substrate Databases. J Chem Inf Model 2016; 56:1228-35. [PMID: 27247997 PMCID: PMC4926231 DOI: 10.1021/acs.jcim.6b00064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 01/11/2023]
Abstract
Protease substrate profiling has nowadays almost become a routine task for experimentalists, and the knowledge on protease peptide substrates is easily accessible via the MEROPS database. We present a shape-based virtual screening workflow using vROCS that applies the information about the specificity of the proteases to find new small-molecule inhibitors. Peptide substrate sequences for three to four substrate positions of each substrate from the MEROPS database were used to build the training set. Two-dimensional substrate sequences were converted to three-dimensional conformations through mutation of a template peptide substrate. The vROCS query was built from single amino acid queries for each substrate position considering the relative frequencies of the amino acids. The peptide-substrate-based shape-based virtual screening approach gives good performance for the four proteases thrombin, factor Xa, factor VIIa, and caspase-3 with the DUD-E data set. The results show that the method works for protease targets with different specificity profiles as well as for targets with different active-site mechanisms. As no structure of the target and no information on small-molecule inhibitors are required to use our approach, the method has significant advantages in comparison with conventional structure- and ligand-based methods.
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Affiliation(s)
- Birgit
J. Waldner
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 82, 6020 Innsbruck, Austria
| | - Julian E. Fuchs
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 82, 6020 Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 82, 6020 Innsbruck, Austria
| | | | - Klaus R. Liedl
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 82, 6020 Innsbruck, Austria
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26
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Arguello Casteleiro M, Klein J, Stevens R. The Proteasix Ontology. J Biomed Semantics 2016; 7:33. [PMID: 27259807 PMCID: PMC4893253 DOI: 10.1186/s13326-016-0078-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) Methods The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. Results The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. Availability The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO. This ontology is free and open for use by everyone. Electronic supplementary material The online version of this article (doi:10.1186/s13326-016-0078-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Julie Klein
- Institut National de la Sante et de la Recherche Medicale (INSERM), U1048, Toulouse, 24105, France
| | - Robert Stevens
- School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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27
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Biniossek ML, Niemer M, Maksimchuk K, Mayer B, Fuchs J, Huesgen PF, McCafferty DG, Turk B, Fritz G, Mayer J, Haecker G, Mach L, Schilling O. Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics. Mol Cell Proteomics 2016; 15:2515-24. [PMID: 27122596 DOI: 10.1074/mcp.o115.056671] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/17/2023] Open
Abstract
We present protease specificity profiling based on quantitative proteomics in combination with proteome-derived peptide libraries. Peptide libraries are generated by endoproteolytic digestion of proteomes without chemical modification of primary amines before exposure to a protease under investigation. After incubation with a test protease, treated and control libraries are differentially isotope-labeled using cost-effective reductive dimethylation. Upon analysis by liquid chromatography-tandem mass spectrometry, cleavage products of the test protease appear as semi-specific peptides that are enriched for the corresponding isotope label. We validate our workflow with two proteases with well-characterized specificity profiles: trypsin and caspase-3. We provide the first specificity profile of a protease encoded by a human endogenous retrovirus and for chlamydial protease-like activity factor (CPAF). For CPAF, we also highlight the structural basis of negative subsite cooperativity between subsites S1 and S2'. For A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) -4, -5, and -15, we show a canonical preference profile, including glutamate in P1 and glycine in P3'. In total, we report nearly 4000 cleavage sites for seven proteases. Our protocol is fast, avoids enrichment or synthesis steps, and enables probing for lysine selectivity as well as subsite cooperativity. Due to its simplicity, we anticipate usability by most proteomic laboratories.
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Affiliation(s)
| | - Melanie Niemer
- §Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Bettina Mayer
- From the ‡Institute of Molecular Medicine and Cell Research
| | | | - Pitter F Huesgen
- **Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Forschungszentrum Jülich, 52425 Jülich, Germany
| | | | - Boris Turk
- ‡‡Department of Chemistry, Duke University, Medical Center, Durham, NC 27708, USA; Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Guenther Fritz
- §§Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia; Department of Human Genetics and Center of Human and Molecular Biology, Medical Faculty, University of Saarland Homburg, Germany
| | | | | | - Lukas Mach
- §Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Oliver Schilling
- From the ‡Institute of Molecular Medicine and Cell Research, ‡‡‡BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany; §§§German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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28
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Rawlings ND. Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation. Biochimie 2016; 122:5-30. [PMID: 26455268 PMCID: PMC4756867 DOI: 10.1016/j.biochi.2015.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/05/2015] [Indexed: 11/11/2022]
Abstract
One peptidase can usually be distinguished from another biochemically by its action on proteins, peptides and synthetic substrates. Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages. The total number of peptidases for which at least one cleavage is known is 1700 out of a total of 2457 different peptidases. This paper describes how the cleavages are obtained from the scientific literature, how they are annotated and how cleavages in peptides and proteins are cross-referenced to entries in the UniProt protein sequence database. The specificity profiles of 556 peptidases are shown for which ten or more substrate cleavages are known. However, it has been proposed that at least 40 cleavages in disparate proteins are required for specificity analysis to be meaningful, and only 163 peptidases (6.6%) fulfil this criterion. Also described are the various displays shown on the website to aid with the understanding of peptidase specificity, which are derived from the substrate cleavage collection. These displays include a logo, distribution matrix, and tables to summarize which amino acids or groups of amino acids are acceptable (or not acceptable) in each substrate binding pocket. For each protein substrate, there is a display to show how it is processed and degraded. Also described are tools on the website to help with the assessment of the physiological relevance of cleavages in a substrate. These tools rely on the hypothesis that a cleavage site that is conserved in orthologues is likely to be physiologically relevant, and alignments of substrate protein sequences are made utilizing the UniRef50 database, in which in each entry sequences are 50% or more identical. Conservation in this case means substitutions are permitted only if the amino acid is known to occupy the same substrate binding pocket from at least one other substrate cleaved by the same peptidase.
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Affiliation(s)
- Neil D Rawlings
- Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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29
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Eckhard U, Huesgen PF, Schilling O, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, auf dem Keller U, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14. Data Brief 2016; 7:299-310. [PMID: 26981551 PMCID: PMC4777984 DOI: 10.1016/j.dib.2016.02.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 11/19/2022] Open
Abstract
The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites) to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015) [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number PXD002265.
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Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Pitter F. Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Oliver Schilling
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Caroline L. Bellac
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Georgina S. Butler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer H. Cox
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Antoine Dufour
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Verena Goebeler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich auf dem Keller
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Theo Klein
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F. Lange
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Charlotte J. Morrison
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David Rodriguez
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Amanda E. Starr
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yili Wang
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M. Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- Corresponding author at: Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British ColumbiaVancouverBCCanada
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30
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Waldner BJ, Fuchs JE, Huber RG, von Grafenstein S, Schauperl M, Kramer C, Liedl KR. Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases. J Phys Chem B 2016; 120:299-308. [PMID: 26709959 PMCID: PMC4724848 DOI: 10.1021/acs.jpcb.5b10637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Members of the same protease family
show different substrate specificity,
even if they share identical folds, depending on the physiological
processes they are part of. Here, we investigate the key factors for
subpocket and global specificity of factor Xa, elastase, and granzyme
B which despite all being serine proteases and sharing the chymotrypsin-fold
show distinct substrate specificity profiles. We determined subpocket
interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket
interaction potentials determined for static X-ray structures turned
out to be insufficient to explain serine protease specificity for
all subpockets. Therefore, we generated conformational ensembles using
molecular dynamics simulations. We identified representative binding
site conformations using distance-based hierarchical agglomerative
clustering and determined subpocket interaction potentials for each
representative conformation of the binding site. Considering the differences
in subpocket interaction potentials for these representative conformations
as well as their abundance allowed us to quantitatively explain subpocket
specificity for the nonprime side for all three example proteases
on a molecular level. The methods to identify key regions determining
subpocket specificity introduced in this study are directly applicable
to other serine proteases, and the results provide starting points
for new strategies in rational drug design.
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Affiliation(s)
- Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Roland G Huber
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Bioinformatics Institute (BII), Agency of Science, Technology and Research (A* STAR) , 30 Biopolis Street, Matrix#07-01, 138671 Singapore
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
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31
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Bioanalytical approaches to assess the proteolytic stability of therapeutic fusion proteins. Bioanalysis 2015; 7:3035-51. [DOI: 10.4155/bio.15.217] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Therapeutic fusion proteins (TFPs) are designed to improve the therapeutic profile of an endogenous protein or protein fragment with a limited dose frequency providing the desired pharmacological activity in vivo. Fusion of a therapeutic protein to a half-life extension or targeting domain can improve the disposition of the molecule or introduce a novel mechanism of action. Prolonged exposure and altered biodistribution of an endogenous protein through fusion technology increases the potential for local protein unfolding during circulation increasing the chance for partial proteolysis of the therapeutic domain. Characterizing the proteolytic liabilities of a TFP can guide engineering efforts to inhibit or hinder partial proteolysis. This review focuses on considerations and techniques for evaluating the stability of a TFP both in vivo and in vitro.
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32
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Fuchs JE, Wellenzohn B, Weskamp N, Liedl KR. Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. J Chem Inf Model 2015; 55:2315-23. [PMID: 26501781 PMCID: PMC4658635 DOI: 10.1021/acs.jcim.5b00476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Biopharmaceuticals hold great promise
for the future of drug discovery.
Nevertheless, rational drug design strategies are mainly focused on
the discovery of small synthetic molecules. Herein we present matched
peptides, an innovative analysis technique for biological data related
to peptide and protein sequences. It represents an extension of matched
molecular pair analysis toward macromolecular sequence data and allows
quantitative predictions of the effect of single amino acid substitutions
on the basis of statistical data on known transformations. We demonstrate
the application of matched peptides to a data set of major histocompatibility
complex class II peptide ligands and discuss the trends captured with
respect to classical quantitative structure–activity relationship
approaches as well as structural aspects of the investigated protein–peptide
interface. We expect our novel readily interpretable tool at the interface
of cheminformatics and bioinformatics to support the rational design
of biopharmaceuticals and give directions for further development
of the presented methodology.
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Affiliation(s)
- Julian E Fuchs
- Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Bernd Wellenzohn
- Research Germany/Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG , Birkendorfer Straße 65, 88397 Biberach an der Riss, Germany
| | - Nils Weskamp
- Research Germany/Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG , Birkendorfer Straße 65, 88397 Biberach an der Riss, Germany
| | - Klaus R Liedl
- Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
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33
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Characterizing Protease Specificity: How Many Substrates Do We Need? PLoS One 2015; 10:e0142658. [PMID: 26559682 PMCID: PMC4641643 DOI: 10.1371/journal.pone.0142658] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022] Open
Abstract
Calculation of cleavage entropies allows to quantify, map and compare protease substrate specificity by an information entropy based approach. The metric intrinsically depends on the number of experimentally determined substrates (data points). Thus a statistical analysis of its numerical stability is crucial to estimate the systematic error made by estimating specificity based on a limited number of substrates. In this contribution, we show the mathematical basis for estimating the uncertainty in cleavage entropies. Sets of cleavage entropies are calculated using experimental cleavage data and modeled extreme cases. By analyzing the underlying mathematics and applying statistical tools, a linear dependence of the metric in respect to 1/n was found. This allows us to extrapolate the values to an infinite number of samples and to estimate the errors. Analyzing the errors, a minimum number of 30 substrates was found to be necessary to characterize substrate specificity, in terms of amino acid variability, for a protease (S4-S4’) with an uncertainty of 5 percent. Therefore, we encourage experimental researchers in the protease field to record specificity profiles of novel proteases aiming to identify at least 30 peptide substrates of maximum sequence diversity. We expect a full characterization of protease specificity helpful to rationalize biological functions of proteases and to assist rational drug design.
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34
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Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin. PLoS One 2015; 10:e0140713. [PMID: 26496636 PMCID: PMC4619833 DOI: 10.1371/journal.pone.0140713] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/28/2015] [Indexed: 12/01/2022] Open
Abstract
Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.
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35
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Fuchs JE, Bender A, Glen RC. Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. Mol Inform 2015; 34:626-633. [PMID: 26435758 PMCID: PMC4583778 DOI: 10.1002/minf.201400166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/16/2014] [Indexed: 11/12/2022]
Abstract
The Centre for Molecular Informatics, formerly Unilever Centre for Molecular Science Informatics (UCMSI), at the University of Cambridge is a world-leading driving force in the field of cheminformatics. Since its opening in 2000 more than 300 scientific articles have fundamentally changed the field of molecular informatics. The Centre has been a key player in promoting open chemical data and semantic access. Though mainly focussing on basic research, close collaborations with industrial partners ensured real world feedback and access to high quality molecular data. A variety of tools and standard protocols have been developed and are ubiquitous in the daily practice of cheminformatics. Here, we present a retrospective of cheminformatics research performed at the UCMSI, thereby highlighting historical and recent trends in the field as well as indicating future directions.
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Affiliation(s)
- Julian E Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW, UK phone/fax: +44 (0)1223 336472/+44 (0)1223 763076
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW, UK phone/fax: +44 (0)1223 336472/+44 (0)1223 763076
| | - Robert C Glen
- Centre for Molecular Informatics, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW, UK phone/fax: +44 (0)1223 336472/+44 (0)1223 763076
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36
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Abstract
Catalytically inactive enzymes (also known as pseudoproteases, protease homologues or paralogues, non-peptidase homologues, non-enzymes and pseudoenzymes) have traditionally been hypothesized to act as regulators of their active homologues. However, those that have been characterized demonstrate that inactive enzymes have an extensive and expanding role in biological processes, including regulation, inhibition and immune modulation. With the emergence of each new genome, more inactive enzymes are being identified, and their abundance and potential as therapeutic targets has been realized. In the light of the growing interest in this emerging field the present review focuses on the classification, structure, function and mechanism of inactive enzymes. Examples of how inactivity is defined, how this is reflected in the structure, functions of inactive enzymes in biological processes and their mode of action are discussed.
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37
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Hartmann A, Gostner J, Fuchs JE, Chaita E, Aligiannis N, Skaltsounis L, Ganzera M. Inhibition of Collagenase by Mycosporine-like Amino Acids from Marine Sources. PLANTA MEDICA 2015; 81:813-820. [PMID: 26039265 PMCID: PMC4515944 DOI: 10.1055/s-0035-1546105] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Matrix metalloproteinases play an important role in extracellular matrix remodeling. Excessive activity of these enzymes can be induced by UV light and leads to skin damage, a process known as photoaging. In this study, we investigated the collagenase inhibition potential of mycosporine-like amino acids, compounds that have been isolated from marine organisms and are known photoprotectants against UV-A and UV-B. For this purpose, the commonly used collagenase assay was optimized and for the first time validated in terms of relationships between enzyme-substrate concentrations, temperature, incubation time, and enzyme stability. Three compounds were isolated from the marine red algae Porphyra sp. and Palmaria palmata, and evaluated for their inhibitory properties against Chlostridium histolyticum collagenase. A dose-dependent, but very moderate, inhibition was observed for all substances and IC50 values of 104.0 µM for shinorine, 105.9 µM for porphyra, and 158.9 µM for palythine were determined. Additionally, computer-aided docking models suggested that the mycosporine-like amino acids binding to the active site of the enzyme is a competitive inhibition.
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Affiliation(s)
- Anja Hartmann
- Institute of Pharmacy, Pharmacognosy, University of Innsbruck, 6020 Innsbruck, Austria
| | - Johanna Gostner
- Medical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Julian E. Fuchs
- Center for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Eliza Chaita
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, University of Athens, Athens 15771, Greece
| | - Nektarios Aligiannis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, University of Athens, Athens 15771, Greece
| | - Leandros Skaltsounis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, University of Athens, Athens 15771, Greece
| | - Markus Ganzera
- Institute of Pharmacy, Pharmacognosy, University of Innsbruck, 6020 Innsbruck, Austria
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Fuchs JE, Waldner BJ, Huber RG, von Grafenstein S, Kramer C, Liedl KR. Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding. J Chem Theory Comput 2015; 11:851-60. [DOI: 10.1021/ct500633u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Julian E. Fuchs
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Birgit J. Waldner
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Roland G. Huber
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
- Bioinformatics
Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, 138671 Singapore
| | - Susanne von Grafenstein
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Christian Kramer
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
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Rawlings ND, Barrett AJ, Bateman A. Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates. ACTA ACUST UNITED AC 2014; 48:1.25.1-1.25.33. [PMID: 25501939 DOI: 10.1002/0471250953.bi0125s48] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MEROPS is a database of proteolytic enzymes as well as their inhibitors and substrates. Proteolytic enzymes and protein inhibitors are organized into protein domain families. In turn, families are organized into clans. Each peptidase, inhibitor, family, and clan has associated annotation, a multiple sequence alignment, a phylogenetic tree, literature references, and links to other databases. Interactions between proteolytic enzymes and inhibitors and between proteolytic enzymes and substrates are also presented. The entries in MEROPS are available via the World Wide Web. This unit contains detailed information on how to access and utilize the information present in the MEROPS database. Details on running MEROPS both remotely and locally are presented.
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Affiliation(s)
- Neil D Rawlings
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Duchêne D, Colombo E, Désilets A, Boudreault PL, Leduc R, Marsault E, Najmanovich R. Analysis of Subpocket Selectivity and Identification of Potent Selective Inhibitors for Matriptase and Matriptase-2. J Med Chem 2014; 57:10198-204. [DOI: 10.1021/jm5015633] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dominic Duchêne
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Eloïc Colombo
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Antoine Désilets
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Richard Leduc
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Eric Marsault
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Rafael Najmanovich
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
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Dai D, Huang Q, Nussinov R, Ma B. Promiscuous and specific recognition among ephrins and Eph receptors. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:1729-40. [PMID: 25017878 PMCID: PMC4157952 DOI: 10.1016/j.bbapap.2014.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 01/04/2023]
Abstract
Eph-ephrin interactions control the signal transduction between cells and play an important role in carcinogenesis and other diseases. The interactions between Eph receptors and ephrins of the same subclass are promiscuous; there are cross-interactions between some subclasses, but not all. To understand how Eph-ephrin interactions can be both promiscuous and specific, we investigated sixteen energy landscapes of four Eph receptors (A2, A4, B2, and B4) interacting with four ephrin ligands (A1, A2, A5, and B2). We generated conformational ensembles and recognition energy landscapes starting from separated Eph and ephrin molecules and proceeding up to the formation of Eph-ephrin complexes. Analysis of the Eph-ephrin recognition trajectories and the co-evolution entropy of 400 ligand binding domains of Eph receptor and 241 ephrin ligands identified conserved residues during the recognition process. Our study correctly predicted the promiscuity and specificity of the interactions and provided insights into their recognition. The dynamic conformational changes during Eph-ephrin recognition can be described by progressive conformational selection and population shift events, with two dynamic salt bridges between EphB4 and ephrin-B2 contributing to the specific recognition. EphA3 cancer-related mutations lowered the binding energies. The specificity is not only controlled by the final stage of the interaction across the protein-protein interface, but also has large contributions from binding kinetics with the help of dynamic intermediates along the pathway from the separated Eph and ephrin to the Eph-ephrin complex.
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Affiliation(s)
- Dandan Dai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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Fuchs JE, Liedl KR. Substrate sequences tell similar stories as binding cavities: commentary. J Chem Inf Model 2014; 53:3115-6. [PMID: 24359119 PMCID: PMC3871284 DOI: 10.1021/ci4005783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80/82, A-6020 Innsbruck, Austria
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Filip S, Pontillo C, Peter Schanstra J, Vlahou A, Mischak H, Klein J. Urinary proteomics and molecular determinants of chronic kidney disease: possible link to proteases. Expert Rev Proteomics 2014; 11:535-48. [DOI: 10.1586/14789450.2014.926224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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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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Fuchs JE, von Grafenstein S, Huber RG, Wallnoefer HG, Liedl KR. Specificity of a protein-protein interface: local dynamics direct substrate recognition of effector caspases. Proteins 2013; 82:546-55. [PMID: 24085488 PMCID: PMC4282588 DOI: 10.1002/prot.24417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 12/29/2022]
Abstract
Proteases are prototypes of multispecific protein–protein interfaces. Proteases recognize and cleave protein and peptide substrates at a well-defined position in a substrate binding groove and a plethora of experimental techniques provide insights into their substrate recognition. We investigate the caspase family of cysteine proteases playing a key role in programmed cell death and inflammation, turning caspases into interesting drug targets. Specific ligand binding to one particular caspase is difficult to achieve, as substrate specificities of caspase isoforms are highly similar. In an effort to rationalize substrate specificity of two closely related caspases, we investigate the substrate promiscuity of the effector Caspases 3 and 7 by data mining (cleavage entropy) and by molecular dynamics simulations. We find a strong correlation between binding site rigidity and substrate readout for individual caspase subpockets explaining more stringent substrate readout of Caspase 7 via its narrower conformational space. Caspase 3 subpockets S3 and S4 show elevated local flexibility explaining the more unspecific substrate readout of that isoform in comparison to Caspase 7. We show by in silico exchange mutations in the S3 pocket of the proteases that a proline residue in Caspase 7 contributes to the narrowed conformational space of the binding site. These findings explain the substrate specificities of caspases via a mechanism of conformational selection and highlight the crucial importance of binding site local dynamics in substrate recognition of proteases. Proteins 2014; 82:546–555.
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Affiliation(s)
- Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
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