8
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Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022; 14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.
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Affiliation(s)
- Rahul Khetan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | | | - Uddipan Kar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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9
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Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun 2021; 12:6947. [PMID: 34845212 PMCID: PMC8630030 DOI: 10.1038/s41467-021-27222-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/02/2021] [Indexed: 01/14/2023] Open
Abstract
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Steven M Lewis
- Cyrus Biotechnology, 1201 Second Ave, Suite 900, Seattle, WA, 98101, USA
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA
| | - Rebecca F Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kyle Barlow
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Ziv Ben-Aharon
- Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel
| | - Daniel Farrell
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Jason Fell
- Genome Center, University of California, Davis, CA, 95616, USA
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - William A Hansen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
| | - Ameya Harmalkar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeliazko Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany
| | - Justyna D Krys
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amanda L Loshbaugh
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jack Maguire
- Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA
| | - Morgan L Nance
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Phuong T Nguyen
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frank Teets
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Johanna K S Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark
| | - Andrew Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Hope Woods
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA
| | - Brahm J Yachnin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | | | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason W Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany
| | - William Schief
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel
| | - Justin B Siegel
- Genome Center, University of California, Davis, CA, 95616, USA
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Brian Kuhlman
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Andrew Leaver-Fay
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.
- Department of Biology, New York University, New York, NY, 10003, USA.
- Department of Computer Science, New York University, New York, NY, 10003, USA.
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