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Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023; 247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.
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Affiliation(s)
- Jiaqi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiewen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Haibin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yili Wu
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Oujiang Laboratory, Wenzhou, Zhejiang 325035, China
| | - Shuxian Meng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Ping Wang
- New Technology R&D Department, Tianjin Modern Innovative TCM Technology Company Limited, Tianjin 300392, China
| | - Miao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; China Resources Biopharmaceutical Company Limited, Beijing 100029, China
| | - Yuli Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Tianjin Pharmaceutical Da Ren Tang Group Corporation Limited, Traditional Chinese Pharmacy Research Institute, Tianjin Key Laboratory of Quality Control in Chinese Medicine, Tianjin 300457, China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Yuanhang Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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Mrigwani A, Pitaliya M, Kaur H, Kasilingam B, Thakur B, Guptasarma P. Rational mutagenesis of Thermobifida fusca cutinase to modulate the enzymatic degradation of polyethylene terephthalate. Biotechnol Bioeng 2023; 120:674-686. [PMID: 36514261 DOI: 10.1002/bit.28305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Thermobifida fusca cutinase (TfCut2) is a carboxylesterase (CE) which degrades polyethylene terephthalate (PET) as well as its degradation intermediates [such as oligoethylene terephthalate (OET), or bis-/mono-hydroxyethyl terephthalate (BHET/MHET)] into terephthalic acid (TPA). Comparisons of the surfaces of certain CEs (including TfCut2) were combined with docking and molecular dynamics simulations involving 2HE-(MHET)3, a three-terephthalate OET, to support the rational design of 22 variants with potential for improved generation of TPA from PET, comprising 15 single mutants (D12L, E47F, G62A, L90A, L90F, H129W, W155F, ΔV164, A173C, H184A, H184S, F209S, F209I, F249A, and F249R), 6 double mutants [H129W/T136S, A173C/A206C, A173C/A210C, G62A/L90F, G62A/F209I, and G62A/F249R], and 1 triple mutant [G62A/F209I/F249R]. Of these, nine displayed no activity, three displayed decreased activity, three displayed comparable activity, and seven displayed increased (~1.3- to ~7.2-fold) activity against solid PET, while all variants displayed activity against BHET. Of the variants that displayed increased activity against PET, four displayed more activity than G62A, the most-active mutant of TfCut2 known till date. Of these four, three displayed even more activity than LCC (G62A/F209I, G62A/F249R, and G62A/F209I/F249R), a CE known to be ~5-fold more active than wild-type TfCut2. These improvements derived from changes in PET binding and not changes in catalytic efficiency.
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Affiliation(s)
- Arpita Mrigwani
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Madhav Pitaliya
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Harman Kaur
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Bharathraj Kasilingam
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Bhishem Thakur
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
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Abe I, Tagami U, Kashiwagi T, Sugiyama M, Suzuki SI, Takagi H, Yokozeki K. Screening of α-amino acid ester acyl transferase variant with improved activity by combining rational and random mutagenesis. J Biochem 2022; 173:43-52. [PMID: 36260086 DOI: 10.1093/jb/mvac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 12/29/2022] Open
Abstract
Random and rational mutagenesis of an α-amino acid ester acyl transferase from Sphingobacterium siyangensis AJ2458 (SAET) was conducted to examine the production of aspartame, an α-l-aspartyl-l-phenylalanine methyl ester. We previously reported aspartame production via combination of enzymatic and chemical methods. However, the productivity of the aspartame intermediate by SAET was approximately one-fifth that of l-alanyl-l-glutamine (Ala-Gln), whose production method has already been established. Here, to improve the enzymatic activity of SAET, we performed random mutagenesis in the gene encoding SAET and obtained 10 mutations that elevated the enzymatic activity (1.2- to 1.7-fold increase) relative to that of wild-type SAET. To further improve the activity, we performed mutagenesis to optimize the combination of the obtained mutations and finally selected one SAET variant with 10 amino acid substitutions (M35-4 SAET). An Escherichia coli strain overexpressing M35-4 SAET displayed a 5.7-fold higher activity than that of the wild-type SAET, which was almost equal to that of Ala-Gln by an E. coli strain overexpressing wild-type SAET. The Vmax value of M35-4 SAET was 2.0-fold greater, and its thermostability was higher than those of wild-type SAET. These results suggest that the obtained SAET variants contribute to improvement in aspartame production.
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Affiliation(s)
- Isao Abe
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan.,Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Uno Tagami
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Tatsuki Kashiwagi
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Masakazu Sugiyama
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Shun-Ichi Suzuki
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Kenzo Yokozeki
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
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Orlando M, Fortuna S, Oloketuyi S, Bajc G, Goldenzweig A, de Marco A. CDR1 Composition Can Affect Nanobody Recombinant Expression Yields. Biomolecules 2021; 11:biom11091362. [PMID: 34572576 PMCID: PMC8465892 DOI: 10.3390/biom11091362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
The isolation of nanobodies from pre-immune libraries by means of biopanning is a straightforward process. Nevertheless, the recovered candidates often require optimization to improve some of their biophysical characteristics. In principle, CDRs are not mutated because they are likely to be part of the antibody paratope, but in this work, we describe a mutagenesis strategy that specifically addresses CDR1. Its sequence was identified as an instability hot spot by the PROSS program, and the available structural information indicated that four CDR1 residues bound directly to the antigen. We therefore modified the loop flexibility with the addition of an extra glycine rather than by mutating single amino acids. This approach significantly increased the nanobody yields but traded-off with moderate affinity loss. Accurate modeling coupled with atomistic molecular dynamics simulations enabled the modifications induced by the glycine insertion and the rationale behind the engineering design to be described in detail.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100 Varese, Italy;
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia;
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
- Correspondence: ; Tel.: +386-(05)-3315295
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Van Overtveldt S, Da Costa M, Gevaert O, Joosten HJ, Beerens K, Desmet T. Determinants of the Nucleotide Specificity in the Carbohydrate Epimerase Family 1. Biotechnol J 2020; 15:e2000132. [PMID: 32761842 DOI: 10.1002/biot.202000132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/20/2020] [Indexed: 11/09/2022]
Abstract
In recent years, carbohydrate epimerases have attracted increasing attention as promising biocatalysts for the production of specialty sugars and derivatives. The vast majority of these enzymes are active on nucleotide-activated sugars, rather than on their free counterparts. Although such epimerases are known to have a clear preference for a particular nucleotide (UDP, GDP, CDP, or ADP), very little is known about the determinants of the respective specificities. In this work, sequence motifs are identified that correlate with the different nucleotide specificities in one of the main epimerase superfamilies, carbohydrate epimerase 1 (CEP1). To confirm their relevance, GDP- and CDP-specific residues are introduced into the UDP-glucose 4-epimerase from Thermus thermophilus, resulting in a 3-fold and 13-fold reduction in KM for GDP-Glc and CDP-Glc, respectively. Moreover, several variants are severely crippled in UDP-Glc activity, which further underlines the crucial role of the identified positions. Hence, the analysis should prove to be valuable for the further exploration and application of epimerases involved in carbohydrate synthesis.
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Affiliation(s)
- Stevie Van Overtveldt
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Matthieu Da Costa
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, Nijmegen, 6511 AA, The Netherlands
| | - Koen Beerens
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
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Serrano A, Arilla-Luna S, Medina M. Insights into the FMNAT Active Site of FAD Synthase: Aromaticity is Essential for Flavin Binding and Catalysis. Int J Mol Sci 2020; 21:E3738. [PMID: 32466340 DOI: 10.3390/ijms21103738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 11/17/2022] Open
Abstract
The last step in the biosynthesis of flavin adenine dinucleotide (FAD) is considered a target for the design of antimicrobial drugs because it is carried out by two non-homologous proteins in eukaryotic and prokaryotic organisms. Monofunctional FMN: adenylyltransferases (FMNAT) in Eukarya and FMNAT modules of bifunctional FAD synthases (FADS) in Prokarya belong to different structural families with dissimilar chemistry and binding modes for the substrates. In this study, we analyzed the relevance of the hydrophobic environment of the flavin isoalloxazine in the FMNAT active site of Corynebacterium ammoniagenes FADS (CaFADS) through the mutational analysis of its F62, Y106, and F128 residues. They form the isoalloxazine binding cavity and are highly conserved in the prokaryotic FADS family. The spectroscopic, steady-state kinetics and thermodynamic data presented indicate that distortion of aromaticity at the FMNAT isoalloxazine binding cavity prevents FMN and FAD from correct accommodation in their binding cavity and, as a consequence, decreases the efficiency of the FMNAT activity. Therefore, the side-chains of F62, Y106 and F128 are relevant in the formation of the catalytic competent complex during FMNAT catalysis in CaFADS. The introduced mutations also modulate the activity occurring at the riboflavin kinase (RFK) module of CaFADS, further evidencing the formation of quaternary assemblies during catalysis.
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Knopp GW, Stadlmayr G, Ruker F. IgG Fc Fragment as a Scaffold for Development of Targeted Therapeutics. Curr Pharm Biotechnol 2016; 17:1315-1323. [PMID: 27842481 DOI: 10.2174/1389201018666161114152527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/17/2015] [Accepted: 11/03/2016] [Indexed: 11/22/2022]
Abstract
Monoclonal antibodies and Fc fusion proteins have been successful therapeutics in the field of cancer and immune disease. As their pharmacological activity is dependent on the Fc fragment governing their effector functions and long in vivo half-life, the extensive engineering of the Fc for altered binding of its natural ligands that enable these properties has delivered molecules optimized for their therapeutic effect. Recently, the IgG1 Fc region itself and its subunits monomeric Fc fragment, CH2 and monomeric CH3 domain, have been engineered into scaffolds with favorable biophysical properties and a high potential for de novo antigen recognition. A dimeric Fc fragment with an antigen binding site has proven suitable for evaluation in animal models and has already entered human trials. Such modified constant domains can easily be incorporated into an antibody or fused with antibody domains of a second specificity. The small size of the Fc and its subunits that enhances their tissue penetration, as well as the unique topology of their binding sites that allows novel modes of contact with the antigen, are attractive features that prompt their development into promising candidate therapeutics.
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Affiliation(s)
| | | | - Florian Ruker
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Christian Doppler Laboratory for Innovative Immunotherapeutics, Muthgasse 18, 1190 Vienna, Austria.. Austria
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