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Liu Y, Tsang K, Mays M, Hansen G, Chiecko J, Crames M, Wei Y, Zhou W, Fredrick C, Hu J, Liu D, Gebhard D, Huang ZF, Datar A, Kronkaitis A, Gueneva-Boucheva K, Seeliger D, Han F, Sen S, Kasturirangan S, Scheer JM, Nixon AE, Panavas T, Marlow MS, Kumar S. An adapted consensus protein design strategy for identifying globally optimal biotherapeutics. MAbs 2022; 14:2073632. [PMID: 35613320 PMCID: PMC9135432 DOI: 10.1080/19420862.2022.2073632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Biotherapeutic optimization, whether to improve general properties or to engineer specific attributes, is a time-consuming process with uncertain outcomes. Conversely, Consensus Protein Design has been shown to be a viable approach to enhance protein stability while retaining function. In adapting this method for a more limited number of protein sequences, we studied 21 consensus single-point variants from eight publicly available CD3 binding sequences with high similarity but diverse biophysical and pharmacological properties. All single-point consensus variants retained CD3 binding and performed similarly in cell-based functional assays. Using Ridge regression analysis, we identified the variants and sequence positions with overall beneficial effects on developability attributes of the CD3 binders. A second round of sequence generation that combined these substitutions into a single molecule yielded a unique CD3 binder with globally optimized developability attributes. In this first application to therapeutic antibodies, adapted Consensus Protein Design was found to be highly beneficial within lead optimization, conserving resources and minimizing iterations. Future implementations of this general strategy may help accelerate drug discovery and improve success rates in bringing novel biotherapeutics to market.
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Affiliation(s)
- Yanyun Liu
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Kenny Tsang
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Michelle Mays
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Gale Hansen
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Jeffrey Chiecko
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Maureen Crames
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Yangjie Wei
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Weijie Zhou
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Chase Fredrick
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - James Hu
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Dongmei Liu
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Douglas Gebhard
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Zhong-Fu Huang
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Akshita Datar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Anthony Kronkaitis
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | | | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | - Fei Han
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Saurabh Sen
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Srinath Kasturirangan
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Justin M Scheer
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Andrew E Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Tadas Panavas
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Michael S Marlow
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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Kumar R, Goomber S, Kaur J. Engineering lipases for temperature adaptation: Structure function correlation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140261. [PMID: 31401312 DOI: 10.1016/j.bbapap.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/13/2023]
Abstract
Bacillus lipases are industrially attractive enzymes due to their broad substrate specificity and optimum alkaline pH. However, narrow temperature range of action and low thermostability restrain their optimal use and thus, necessitate attention. Several laboratories are engaged in protein engineering of Bacillus lipases to generate variants with improved attributes for decades using techniques such as directed evolution or rational design. This review summarizes the effect of mutations on the conformational changes through in silico modeling and their manifestation with respect to various biochemical parameters. Various studies have been put together to develop a perspective on the molecular basis of biocatalysis of lipases holding industrial importance.
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Affiliation(s)
- Rakesh Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; Department of Microbiology and Cell Biology, Indian Institute Of Science, Bangalore, Karnataka 560012, India
| | - Shelly Goomber
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; National Institute of Malaria Research, Dwarka, New Delhi, Delhi 110077, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
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Sönmez B, Yanık-Yıldırım KC, Wood TK, Vardar-Schara G. The role of substrate binding pocket residues phenylalanine 176 and phenylalanine 196 on Pseudomonas sp. OX1 toluene o-xylene monooxygenase activity and regiospecificity. Biotechnol Bioeng 2014; 111:1506-12. [PMID: 24519264 DOI: 10.1002/bit.25212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/27/2013] [Accepted: 02/06/2014] [Indexed: 11/10/2022]
Abstract
Saturation mutagenesis was used to generate eleven substitutions of toluene-o-xylene monooxygenase (ToMO) at alpha subunit (TouA) positions F176 and F196 among which nine were novel: F176H, F176N, F176S, F176T, F196A, F196L, F196T, F196Y, F196H, F196I, and F196V. By testing the substrates phenol, toluene, and naphthalene, these positions were found to influence ToMO oxidation activity and regiospecificity. Specifically, TouA variant F176H was identified that had 4.7-, 4.3-, and 1.8-fold faster hydroxylation activity towards phenol, toluene, and naphthalene, respectively, compared to native ToMO. The F176H variant also produced the novel product hydroquinone (61%) from phenol, made twofold more 2-naphthol from naphthalene (34% vs. 16% by the wild-type ToMO), and had the regiospecificity of toluene changed from 51% to 73% p-cresol. The TouA F176N variant had the most para-hydroxylation capability, forming p-cresol (92%) from toluene and hydroquinone (82%) from phenol as the major product, whereas native ToMO formed 30% o-cresol, 19% m-cresol, and 51% of p-cresol from toluene and 100% catechol from phenol. For naphthalene oxidation, TouA variant F176S exhibited the largest shift in the product distribution by producing threefold more 2-naphthol. Among the other F196 variants, F196L produced catechol from phenol two times faster than the wild-type enzyme. The TouA F196I variant produced twofold less o-cresol and 19% more p-cresol from toluene, and the TouA F196A variant produced 62% more 2-naphthol from naphthalene compared to wild-type ToMO. Both of these positions have never been studied through the saturation mutagenesis and some of the best substitutions uncovered here have never been predicted and characterized for aromatics hydroxylation.
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Affiliation(s)
- Burcu Sönmez
- Department of Genetics and Biongineering, Fatih University, Buyukcekmece, Istanbul, 34500, Turkey
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Aerts D, Verhaeghe T, Joosten HJ, Vriend G, Soetaert W, Desmet T. Consensus engineering of sucrose phosphorylase: The outcome reflects the sequence input. Biotechnol Bioeng 2013; 110:2563-72. [DOI: 10.1002/bit.24940] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/30/2013] [Accepted: 04/08/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Dirk Aerts
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| | - Tom Verhaeghe
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| | - Henk-Jan Joosten
- Bio-Prodict; Castellastraat 116; Nijmegen; 6512; EZ; The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics; Radboud University Nijmegen Medical Centre; PO Box 9101; Nijmegen; 6500; HB; The Netherlands
| | - Wim Soetaert
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| | - Tom Desmet
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
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