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Prabakaran R, Rawat P, Kumar S, Gromiha MM. Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets. Brief Bioinform 2021; 22:6309925. [PMID: 34181000 DOI: 10.1093/bib/bbab240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/18/2021] [Accepted: 06/02/2021] [Indexed: 01/09/2023] Open
Abstract
Several prediction algorithms and tools have been developed in the last two decades to predict protein and peptide aggregation. These in silico tools aid to predict the aggregation propensity and amyloidogenicity as well as the identification of aggregation-prone regions. Despite the immense interest in the field, it is of prime importance to systematically compare these algorithms for their performance. In this review, we have provided a rigorous performance analysis of nine prediction tools using a variety of assessments. The assessments were carried out on several non-redundant datasets ranging from hexapeptides to protein sequences as well as amyloidogenic antibody light chains to soluble protein sequences. Our analysis reveals the robustness of the current prediction tools and the scope for improvement in their predictive performances. Insights gained from this work provide critical guidance to the scientific community on advantages and limitations of different aggregation prediction methods and make informed decisions about their research needs.
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Affiliation(s)
| | | | - Sandeep Kumar
- Department of Biotherapeutics Discovery in Boehringer-Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
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Pallarés I, Ventura S. Advances in the Prediction of Protein Aggregation Propensity. Curr Med Chem 2019; 26:3911-3920. [DOI: 10.2174/0929867324666170705121754] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/29/2022]
Abstract
Background:
Protein aggregation into β-sheet-enriched insoluble assemblies is being
found to be associated with an increasing number of debilitating human pathologies, such as Alzheimer’s
disease or type 2 diabetes, but also with premature aging. Furthermore, protein aggregation
represents a major bottleneck in the production and marketing of proteinbased therapeutics.
Thus, the development of methods to accurately forecast the aggregation propensity of a certain
protein is of much value.
Methods/Results:
A myriad of in vitro and in vivo aggregation studies have shown that the aggregation
propensity of a certain polypeptide sequence is highly dependent on its intrinsic properties
and, in most cases, driven by specific short regions of high aggregation propensity. These observations
have fostered the development of a first generation of algorithms aimed to predict protein
aggregation propensities from the protein sequence. A second generation of programs able to map
protein aggregation on protein structures is emerging. Herein, we review the most representative
online accessible predictive tools, emphasizing their main distinctive features and the range of
applications.
Conclusion:
In this review, we describe representative biocomputational approaches to evaluate
the aggregation properties of protein sequences and structures, while illustrating how they can
become very useful tools to target protein aggregation in biomedicine and biotechnology.
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Affiliation(s)
- Irantzu Pallarés
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
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de Marco A, Ferrer-Miralles N, Garcia-Fruitós E, Mitraki A, Peternel S, Rinas U, Trujillo-Roldán MA, Valdez-Cruz NA, Vázquez E, Villaverde A. Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 2019; 43:53-72. [PMID: 30357330 DOI: 10.1093/femsre/fuy038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Vassilika Vouton, 70013 Heraklion, Crete, Greece.,Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology Hellas (FORTH), N. Plastira 100, Vassilika Vouton, 70013 Heraklion, Crete, Greece
| | | | - Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
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Prabakaran R, Goel D, Kumar S, Gromiha MM. Aggregation prone regions in human proteome: Insights from large-scale data analyses. Proteins 2017; 85:1099-1118. [DOI: 10.1002/prot.25276] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/10/2017] [Accepted: 02/24/2017] [Indexed: 12/25/2022]
Affiliation(s)
- R. Prabakaran
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - Dhruv Goel
- Department of Computer Science and Engineering; Motilal Nehru National Institute of Technology; Allahabad 211004 India
| | - Sandeep Kumar
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; 700 Chesterfield Parkway West Chesterfield Missouri 63017, USA
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
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Kumar S, Plotnikov NV, Rouse JC, Singh SK. Biopharmaceutical Informatics: supporting biologic drug development via molecular modelling and informatics. J Pharm Pharmacol 2017; 70:595-608. [DOI: 10.1111/jphp.12700] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/29/2016] [Indexed: 12/23/2022]
Abstract
Abstract
Objectives
The purpose of this article is to introduce an emerging field called ‘Biopharmaceutical Informatics’. It describes how tools from Information technology and Molecular Biophysics can be adapted, developed and gainfully employed in discovery and development of biologic drugs.
Key Findings
The findings described here are based on literature surveys and the authors’ collective experiences in the field of biologic drug product development. A strategic framework to forecast early the hurdles faced during drug product development is weaved together and elucidated using chemical degradation as an example. Efficiency of translating biologic drug discoveries into drug products can be significantly improved by combining learnings from experimental biophysical and analytical data on the drug candidates with molecular properties computed from their sequences and structures via molecular modeling and simulations.
Summary
Biopharmaceutical Informatics seeks to promote applications of computational tools towards discovery and development of biologic drugs. When fully implemented, industry-wide, it will enable rapid materials-free developability assessments of biologic drug candidates at early stages as well as streamline drug product development activities such as commercial scale production, purification, formulation, analytical characterization, safety and in vivo performance.
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Affiliation(s)
- Sandeep Kumar
- Pharmaceutical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, USA
| | - Nikolay V Plotnikov
- Pharmaceutical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, USA
| | - Jason C Rouse
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, MA, USA
| | - Satish K Singh
- Pharmaceutical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, USA
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CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation. PLoS One 2016; 11:e0152949. [PMID: 27043825 PMCID: PMC4820268 DOI: 10.1371/journal.pone.0152949] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/20/2016] [Indexed: 11/24/2022] Open
Abstract
Accurate distinction between peptide sequences that can form amyloid-fibrils or amorphous β-aggregates, identification of potential aggregation prone regions in proteins, and prediction of change in aggregation rate of a protein upon mutation(s) are critical to research on protein misfolding diseases, such as Alzheimer’s and Parkinson’s, as well as biotechnological production of protein based therapeutics. We have developed a Curated Protein Aggregation Database (CPAD), which has collected results from experimental studies performed by scientific community aimed at understanding protein/peptide aggregation. CPAD contains more than 2300 experimentally observed aggregation rates upon mutations in known amyloidogenic proteins. Each entry includes numerical values for the following parameters: change in rate of aggregation as measured by fluorescence intensity or turbidity, name and source of the protein, Uniprot and Protein Data Bank codes, single point as well as multiple mutations, and literature citation. The data in CPAD has been supplemented with five different types of additional information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous β-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are available in the Protein Data Bank (PDB) and (v) Experimentally validated aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is linked to other related databases and resources, such as Uniprot, Protein Data Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with different search and display options so that users have the ability to get the data in multiple ways. CPAD is freely available at http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also been discussed.
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