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Lee KB, Ge X. Generation of Protease Inhibitory Antibodies by Functional In Vivo Selection. Methods Mol Biol 2024; 2747:243-256. [PMID: 38038945 PMCID: PMC10732120 DOI: 10.1007/978-1-0716-3589-6_19] [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] [Indexed: 12/02/2023]
Abstract
Targeting dysregulated protease expression and/or abnormal substrate proteolysis, highly selective inhibition of pathogenic proteases by monoclonal antibodies (mAbs) presents an attractive therapeutic approach for the treatment of diseases including cancer. Herein, we report a functional selection method for protease inhibitory mAbs by periplasmic co-expression of three recombinant proteins-a protease of interest, an antibody Fab library, and a modified β-lactamase TEM-1. We validate this approach by isolation of highly selective and potent mAbs inhibiting human matrix metalloproteinase 9 (MMP9).
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Affiliation(s)
- Ki Baek Lee
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xin Ge
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.
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2
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Choe H, Antee T, Ge X. Substrate derived sequences act as subsite-blocking motifs in protease inhibitory antibodies. Protein Sci 2023; 32:e4691. [PMID: 37278099 PMCID: PMC10285753 DOI: 10.1002/pro.4691] [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: 05/01/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/07/2023]
Abstract
Proteases are involved in many physiologic processes, and dysregulated proteolysis is basis of a variety of diseases. Specific inhibition of pathogenetic proteases via monoclonal antibodies therefore holds significant therapeutic promise. Inspired by the competitive mechanism utilized by many naturally occurring and man-made protease inhibitors, we hypothesized that substrate-like peptide sequences can act as protease subsite blocking motifs if they occupy only one side of the reaction center. To test this hypothesis, a degenerate codon library representing MMP-14 substrate profiles at P1-P5' positions was constructed in the context of an anti-MMP-14 Fab by replacing its inhibitory motif in CDR-H3 with MMP-14 substrate repertoires. After selection for MMP-14 active-site binders by phage panning, results indicated that diverse substrate-like sequences conferring antibodies inhibitory potencies were enriched in the isolated clones. Optimal residues at each of P1-P5' positions were then identified, and the corresponding mutation combinations showed improved characteristics as effective inhibitors of MMP-14. Insights on efficient library designs for inhibitory peptide motifs were further discussed. Overall, this study proved the concept that substrate-derived sequences were able to behave as the inhibitory motifs in protease-specific antibodies. With accumulating data available on protease substrate profiles, we expect the approach described here can be broadly applied to facilitate the generation of antibody inhibitors targeting biomedically important proteases.
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Affiliation(s)
- Hyunjun Choe
- Institute of Molecular MedicineUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
- Department of Chemical and Environmental EngineeringUniversity of California RiversideRiversideCaliforniaUSA
- Present address:
Arrowhead PharmaceuticalsMadisonWIUSA
| | - Tara Antee
- Department of Chemical and Environmental EngineeringUniversity of California RiversideRiversideCaliforniaUSA
| | - Xin Ge
- Institute of Molecular MedicineUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
- Department of Chemical and Environmental EngineeringUniversity of California RiversideRiversideCaliforniaUSA
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3
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Rezhdo A, Lessard CT, Islam M, Van Deventer JA. Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface. Protein Eng Des Sel 2023; 36:gzac017. [PMID: 36648434 PMCID: PMC10365883 DOI: 10.1093/protein/gzac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/20/2022] [Accepted: 11/07/2022] [Indexed: 01/18/2023] Open
Abstract
Display technologies are powerful tools for discovering binding proteins against a broad range of biological targets. However, it remains challenging to adapt display technologies for the discovery of proteins that inhibit the enzymatic activities of targets. Here, we investigate approaches for discovering and characterizing inhibitory antibodies in yeast display format using a well-defined series of constructs and the target matrix metalloproteinase-9. Three previously reported antibodies were used to create model libraries consisting of inhibitory, non-inhibitory, and non-binding constructs. Conditions that preferentially enrich for inhibitory clones were identified for both magnetic bead-based enrichments and fluorescence-activated cell sorting. Half maximal inhibitory concentration (IC50) was obtained through yeast titration assays. The IC50 of the inhibitory antibody obtained in yeast display format falls within the confidence interval of the IC50 value determined in soluble form. Overall, this study identifies strategies for the discovery and characterization of inhibitory clones directly in yeast display format.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Catherine T Lessard
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, USA
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4
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Xu L, Li C, Hua F, Liu X. The CXCL12/CXCR7 signalling axis promotes proliferation and metastasis in cervical cancer. Med Oncol 2021; 38:58. [DOI: 10.1007/s12032-021-01481-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/13/2021] [Indexed: 02/07/2023]
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Nam DH, Lee KB, Kruchowy E, Pham H, Ge X. Protease Inhibition Mechanism of Camelid-like Synthetic Human Antibodies. Biochemistry 2020; 59:3802-3812. [PMID: 32997500 PMCID: PMC7572768 DOI: 10.1021/acs.biochem.0c00690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Macromolecular protease inhibitors and camelid single-domain antibodies achieve their enzymic inhibition functions often through protruded structures that directly interact with catalytic centers of targeted proteases. Inspired by this phenomenon, we constructed synthetic human antibody libraries encoding long CDR-H3s, from which highly selective monoclonal antibodies (mAbs) that inhibit multiple proteases were discovered. To elucidate their molecular mechanisms, we performed in-depth biochemical characterizations on a panel of matrix metalloproteinase (MMP)-14 inhibitory mAbs. Assays included affinity and potency measurements, enzymatic kinetics, a competitive enzyme-linked immunosorbent assay, proteolytic stability, and epitope mapping followed by quantitative analysis of binding energy changes. The results collectively indicated that these mAbs of convex paratopes were competitive inhibitors recognizing the vicinity of the active cleft, with their significant epitopes scattered across the north and south rims of the cleft. Remarkably, identified epitopes were the surface loops that were highly diverse among MMPs and predominately located at the prime side of the proteolytic site, shedding light on the mechanisms of target selectivity and proteolytic resistance. Substrate sequence profiling and paratope mutagenesis further suggested that mAb 3A2 bound to the active-site cleft in a canonical (substrate-like) manner, by direct interactions between 100hNLVATP100m of its CDR-H3 and subsites S1-S5' of MMP-14. Overall, synthetic mAbs carrying convex paratopes can achieve efficient inhibition and thus hold great therapeutic promise for effectively and safely targeting biomedically important proteases.
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Affiliation(s)
- Dong Hyun Nam
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Ki Baek Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Evan Kruchowy
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Henry Pham
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
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Lee KB, Dunn ZS, Lopez T, Mustafa Z, Ge X. Generation of highly selective monoclonal antibodies inhibiting a recalcitrant protease using decoy designs. Biotechnol Bioeng 2020; 117:3664-3676. [PMID: 32716053 DOI: 10.1002/bit.27519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/10/2020] [Accepted: 07/26/2020] [Indexed: 11/11/2022]
Abstract
Matrix metalloproteinase-12 (MMP-12), also known as macrophage elastase, is a potent inflammatory mediator and therefore an important pharmacological target. Clinical trial failures of broad-spectrum compound MMP inhibitors suggested that specificity is the key for a successful therapy. To provide the required selectivity, monoclonal antibody (mAb)-based inhibitors are on the rise. However, poor production of active recombinant human MMP-12 catalytic domain (cdMMP-12) presented a technical hurdle for its inhibitory mAb development. We hypothesized that this problem could be solved by designing an expression-optimized cdMMP-12 mutant without structural disruptions at its reaction cleft and surrounding area, and thus isolated active-site inhibitory mAbs could maintain their binding and inhibition functions toward wild-type MMP-12. We combined three advances in the field-PROSS algorithm for cdMMP-12 mutant design, convex paratope antibody library construction, and functional selection for inhibitory mAbs. As a result, isolated Fab inhibitors showed nanomolar affinity and potency toward cdMMP-12 with high selectivity and high proteolytic stability. Particularly, Fab LH11 targeted the reaction cleft of wild-type cdMMP-12 with 75 nM binding KD and 23 nM inhibition IC50 . We expect that our methods can promote the development of mAbs inhibiting important proteases, many of which are recalcitrant to functional production.
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Affiliation(s)
- Ki Baek Lee
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California
| | - Zachary S Dunn
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California
| | - Tyler Lopez
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California.,Element Biosciences, Inc., San Diego, California
| | - Zahid Mustafa
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California
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Zhong C, Cao MJ, Shu M, Sun LC, Yang HH, Wu GP. Tissue inhibitor of metalloproteinase-2 (TIMP-2) from red seabream (Pagrus major): Molecular cloning and biochemical characterization of highly expressed recombinant protein. FISH & SHELLFISH IMMUNOLOGY 2019; 95:556-563. [PMID: 31693944 DOI: 10.1016/j.fsi.2019.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
The tissue inhibitor of metalloproteinase-2 (TIMP-2) is originally characterized as an endogenous inhibitor of matrix metalloproteinases (MMPs) to response collagenolysis associated with immune challenge. In this study, the cDNA encoding TIMP-2a gene from red seabream (Pagrus major) muscle was cloned. It was 585 bp encoding a putative protein of 194 amino acids, which comprised all recognized functional domains and showed the high identity to TIMP-2as from other teleost fishes, revealing it belongs to TIMP-2a family. Soluble rTIMP-2a was efficiently expressed using a new constructed pPIC9K-rTIMP-2a vector with high inhibitory activity against to MMP-2 and MMP-9. The recombinant TIMP-2a tagged with 6 histidine residues showed the molecular mass of 23 kDa and isoelectric point of 6.50. Furthermore, the 6 disulfide bonds formed by 12 conserved cysteine residues were identified as functional motifs for its structural stability. In addition, rTIMP-2a possessed the high inhibitory activity against gelatinolytic hydrolysis and degradation of type I collagen which induced by endogenous MMPs in muscle. The results revealed the properties and inhibitory function of rTIMP-2a, which may be a pivotal role in regulation gelatinolytic MMPs metabolization during defense mechanism.
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Affiliation(s)
- Chan Zhong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Min Jie Cao
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Mei Shu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Le Chang Sun
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Huan Huan Yang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guo Ping Wu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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Wang J, Boddupalli A, Koelbl J, Nam DH, Ge X, Bratlie KM, Schneider IC. Degradation and Remodeling of Epitaxially Grown Collagen Fibrils. Cell Mol Bioeng 2019; 12:69-84. [PMID: 31007771 PMCID: PMC6472930 DOI: 10.1007/s12195-018-0547-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 08/07/2018] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION— The extracellular matrix (ECM) in the tumor microenvironment contains high densities of collagen that are highly aligned, resulting in directional migration called contact guidance that facilitates efficient migration out of the tumor. Cancer cells can remodel the ECM through traction force controlled by myosin contractility or proteolytic activity controlled by matrix metalloproteinase (MMP) activity, leading to either enhanced or diminished contact guidance. METHODS— Recently, we have leveraged the ability of mica to epitaxially grow aligned collagen fibrils in order to assess contact guidance. In this article, we probe the mechanisms of remodeling of aligned collagen fibrils on mica by breast cancer cells. RESULTS— We show that cells that contact guide with high fidelity (MDA-MB-231 cells) exert more force on the underlying collagen fibrils than do cells that contact guide with low fidelity (MTLn3 cells). These high traction cells (MDA-MB-231 cells) remodel collagen fibrils over hours, pulling so hard that the collagen fibrils detach from the surface, effectively delaminating the entire contact guidance cue. Myosin or MMP inhibition decreases this effect. Interestingly, blocking MMP appears to increase the alignment of cells on these substrates, potentially allowing the alignment through myosin contractility to be uninhibited. Finally, amplification or dampening of contact guidance with respect to a particular collagen fibril organization is seen under different conditions. CONCLUSIONS— Both myosin II contractility and MMP activity allow MDA-MB-231 cells to remodel and eventually destroy epitaxially grown aligned collagen fibrils.
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Affiliation(s)
- Juan Wang
- Present Address: Department of Chemical and Biological Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011-2230 USA
| | - Anuraag Boddupalli
- Present Address: Department of Chemical and Biological Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011-2230 USA
| | - Joseph Koelbl
- Present Address: Department of Chemical and Biological Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011-2230 USA
| | - Dong Hyun Nam
- Department of Chemical Engineering, University of California Riverside, Riverside, CA USA
| | - Xin Ge
- Department of Chemical Engineering, University of California Riverside, Riverside, CA USA
| | - Kaitlin M. Bratlie
- Present Address: Department of Chemical and Biological Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011-2230 USA
- Department of Materials Science and Engineering, Iowa State University, Ames, IA USA
| | - Ian C. Schneider
- Present Address: Department of Chemical and Biological Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011-2230 USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA
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9
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Lee KB, Dunn Z, Ge X. Reducing proteolytic liability of a MMP-14 inhibitory antibody by site-saturation mutagenesis. Protein Sci 2019; 28:643-653. [PMID: 30592555 DOI: 10.1002/pro.3567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 12/31/2022]
Abstract
Playing pivotal roles in tumor growth and metastasis, matrix metalloproteinase-14 (MMP-14) is an important cancer target. Potent inhibitory Fab 3A2 with therapy-desired high selectivity has been isolated from a synthetic antibody library carrying long CDR-H3s. However, like many standard mechanism protease inhibitors, Fab 3A2 can be cleaved by high concentrations of MMP-14 after extended incubation at acidic pH. Edman sequencing of generated 3A2 fragments indicated that cleavage occurred within its CDR-H3 between residues N100h (P1) and L100i (P1'). To improve proteolytic stability of 3A2, three positions adjacent to its cleavage site (P1, P1', and P3') were subjected to site-saturation mutagenesis (SSM). Mutations at P1' (L100i) resulted in loss of inhibition function, while screening of 3A2 Fab mutants at P1 (N100h) or P3' (A100k) positions identified four clones exhibiting improvements in both stability and inhibition potency. The majority of these mutants with improved stability were substitutions to either hydrophobic (Lue, Trp) or basic residues (Arg, Lys, His). Combinations of these beneficial mutations resulted in a double mutant N100hR/A100kR, which prolonged half-life twofold with an inhibition potency KI of 6.6 nM. Enzyme kinetics and competitive ELISA suggested that N100hR/A100kR was a competitive inhibitor overlapping its binding epitope with that of nTIMP-2. This study demonstrated that site-directed mutagenesis at or near the cleavage position reduced proteolytic liability of standard mechanism protease inhibitors especially inhibitory antibodies.
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Affiliation(s)
- Ki Baek Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, California, 92521
| | - Zachary Dunn
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, California, 92521
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, California, 92521
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Barb AW, Falconer DJ, Subedi GP. The Preparation and Solution NMR Spectroscopy of Human Glycoproteins Is Accessible and Rewarding. Methods Enzymol 2018; 614:239-261. [PMID: 30611426 DOI: 10.1016/bs.mie.2018.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The majority of proteins excreted by human cells and borne at the cell surface are modified with carbohydrates. Glycoproteins mediate a wide range of processes and adopt fundamental roles in many diseases. The carbohydrates covalently attached to proteins during maturation in the cell directly impact protein structure and function as integral and indispensable components. However, the ability to study the structure of glycoproteins to high resolution was historically limited by technical barriers including a limited availability of appropriate recombinant protein expression platforms, limited methods to generate compositional homogeneity, and difficulties analyzing glycoprotein composition. Furthermore, glycoproteins and in particular the glycan moieties themselves often exhibit a high degree of conformational heterogeneity. Solution NMR spectroscopy is a powerful tool to study biological macromolecules that is capable of characterizing mobile elements of molecules with atomic-level resolution. Methods to express glycoproteins, incorporate stable isotope labels, and analyze glycoproteins have recently opened new avenues to prepare and investigate glycoproteins. These methods are accessible to many laboratories with experience expressing and purifying proteins from prokaryotic expression hosts.
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Affiliation(s)
- Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States.
| | - Daniel J Falconer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Ganesh P Subedi
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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Lopez T, Chuan C, Ramirez A, Chen KHE, Lorenson MY, Benitez C, Mustafa Z, Pham H, Sanchez R, Walker AM, Ge X. Epitope-specific affinity maturation improved stability of potent protease inhibitory antibodies. Biotechnol Bioeng 2018; 115:2673-2682. [PMID: 30102763 DOI: 10.1002/bit.26814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/26/2022]
Abstract
Targeting effectual epitopes is essential for therapeutic antibodies to accomplish their desired biological functions. This study developed a competitive dual color fluorescence-activated cell sorting (FACS) to maturate a matrix metalloprotease 14 (MMP-14) inhibitory antibody. Epitope-specific screening was achieved by selection on MMP-14 during competition with N-terminal domain of tissue inhibitor of metalloproteinase-2 (TIMP-2) (nTIMP-2), a native inhibitor of MMP-14 binding strongly to its catalytic cleft. 3A2 variants with high potency, selectivity, and improved affinity and proteolytic stability were isolated from a random mutagenesis library. Binding kinetics indicated that the affinity improvements were mainly from slower dissociation rates. In vitro degradation tests suggested the isolated variants had half lives 6-11-fold longer than the wt. Inhibition kinetics suggested they were competitive inhibitors which showed excellent selectivity toward MMP-14 over highly homologous MMP-9. Alanine scanning revealed that they bound to the vicinity of MMP-14 catalytic cleft especially residues F204 and F260, suggesting that the desired epitope was maintained during maturation. When converted to immunoglobulin G, B3 showed 5.0 nM binding affinity and 6.5 nM inhibition potency with in vivo half-life of 4.6 days in mice. In addition to protease inhibitory antibodies, the competitive FACS described here can be applied for discovery and engineering biosimilars, and in general for other circumstances where epitope-specific modulation is needed.
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Affiliation(s)
- Tyler Lopez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Chen Chuan
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Aaron Ramirez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Kuan-Hui E Chen
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California
| | - Mary Y Lorenson
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California
| | - Chris Benitez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Zahid Mustafa
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Henry Pham
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Ramon Sanchez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Ameae M Walker
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California
| | - Xin Ge
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
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12
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Staudacher AH, Liapis V, Brown MP. Selectivity Conversion of Protease Inhibitory Antibodies. Antib Ther 2018; 1:55-63. [PMID: 30406213 PMCID: PMC7990135 DOI: 10.1093/abt/tby008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 11/14/2022] Open
Abstract
Background: Proteases are one of the largest pharmaceutical targets for drug developments. Their dysregulations result in a wide variety of diseases. Because proteolytic networks usually consist of protease family members that share high structural and catalytic homology, distinguishing them using small molecule inhibitors is often challenging. To achieve specific inhibition, this study described a novel approach for the generation of protease inhibitory antibodies. As a proof of concept, we aimed to convert a matrix metalloproteinase (MMP)-14 specific inhibitor to MMP-9 specific inhibitory antibodies with high selectivity. Methods: An error-prone single-chain Fv (scFv) library of an MMP-14 inhibitor 3A2 was generated for yeast surface display. A dual-color competitive FACS was developed for selection on MMP-9 catalytic domain (cdMMP-9) and counter-selection on cdMMP-14 simultaneously, which were fused/conjugated with different fluorophores. Isolated MMP-9 inhibitory scFvs were biochemically characterized by inhibition assays on MMP-2/-9/-12/-14, proteolytic stability tests, inhibition mode determination, competitive ELISA with TIMP-2 (a native inhibitor of MMPs), and paratope mutagenesis assays. Results: We converted an MMP-14 specific inhibitor 3A2 into a panel of MMP-9 specific inhibitory antibodies with dramatic selectivity shifts of 690-4,500 folds. Isolated scFvs inhibited cdMMP-9 at nM potency with high selectivity over MMP-2/-12/-14 and exhibited decent proteolytic stability. Biochemical characterizations revealed that these scFvs were competitive inhibitors binding to cdMMP-9 near its reaction cleft via their CDR-H3s. Conclusions: This study developed a novel approach able to convert the selectivity of inhibitory antibodies among closely related protease family members. This methodology can be directly applied for mAbs inhibiting many proteases of biomedical importance.
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Affiliation(s)
- Alexander H Staudacher
- Translational Oncology Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
| | - Vasilios Liapis
- Translational Oncology Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia
| | - Michael P Brown
- Translational Oncology Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, Australia
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13
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Chen KHE, Chen C, Lopez T, Radecki KC, Bustamante K, Lorenson MY, Ge X, Walker AM. Use of a novel camelid-inspired human antibody demonstrates the importance of MMP-14 to cancer stem cell function in the metastatic process. Oncotarget 2018; 9:29431-29444. [PMID: 30034628 PMCID: PMC6047671 DOI: 10.18632/oncotarget.25654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are considered excellent targets for cancer therapy because of their important roles in multiple aspects of tumor growth and metastatic spread. However, not all MMPs, or even all activities of specific MMPs, promote cancer. Therefore, there is a need for highly specific inhibitors. Monoclonal antibodies provide the potential for the degree of specificity required, but the isolation of antibodies able to inhibit a specific protease with high selectivity is challenging. Proteolysis specificity lies in recognition of the substrate in or around the active site, which generally forms a concave cleft inaccessible by human IgGs. Inspired by camelid antibodies, which have convex paratopes, we have produced a recombinant human IgG, designated 3A2, which binds in the substrate cleft of MMP-14, inhibiting its activity, but not the activity of highly homologous MMPs. In the 4T1 highly metastatic, syngeneic, orthotopic model of breast cancer, IgG 3A2 markedly inhibited growth of the primary tumor, but more importantly reduced metastatic spread to the lungs and liver by 94%. Stem cells in the tumor population expressed twice as much MMP-14 mRNA as bulk tumor cells. In addition to reducing dissemination of tumor stem cells, as would be expected from inhibition of MMP-14's ability to degrade components of the extracellular matrix, IgG 3A2 also inhibited the ability of individual stem cells to proliferate and produce colonies. We conclude that it is possible to produce antibodies with sufficient specificity for development as therapeutics and that IgG 3A2 has therapeutic potential.
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Affiliation(s)
- Kuan-Hui E Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Chuan Chen
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Tyler Lopez
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Kelly C Radecki
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Karissa Bustamante
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Mary Y Lorenson
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Ameae M Walker
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
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Guo L, Zhang F, Zhang C, Hu G, Gao C, Chen X, Liu L. Enhancement of malate production through engineering of the periplasmic rTCA pathway in Escherichia coli. Biotechnol Bioeng 2018; 115:1571-1580. [PMID: 29476618 DOI: 10.1002/bit.26580] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 12/13/2022]
Abstract
The compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency; however, prokaryotes are unicellular organisms that lack membrane-bound organelles. To mimic this natural compartmentalization, we present here the targeting of the reductive tricarboxylic acid (rTCA) pathway to the periplasm to enhance the production of malate. A multigene combination knockout strategy was used to construct a phosphoenolpyruvate (PEP) pool. Then, the genes encoding phosphoenolpyruvate carboxykinase and malate dehydrogenase were combinatorially overexpressed to construct a cytoplasmic rTCA pathway for malate biosynthesis; however, the efficiency of malate production was low. To further enhance malate production, the rTCA pathway was targeted to the periplasm, which led to a 100% increase in malate production to 18.8 mM. Next, dual metabolic engineering regulation was adopted to balance the cytoplasmic and periplasmic pathways, leading to an increase in malate production to 58.8 mM. The final engineered strain, GL2306, produced 193 mM malate with a yield of 0.53 mol/mol in 5 L of pH-stat fed-batch culture. The strategy described here paves the way for the development of metabolic engineering and synthetic biology in the microbial production of chemicals.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Fan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Can Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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15
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Nuhn JAM, Perez AM, Schneider IC. Contact guidance diversity in rotationally aligned collagen matrices. Acta Biomater 2018; 66:248-257. [PMID: 29196116 PMCID: PMC5750117 DOI: 10.1016/j.actbio.2017.11.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 12/16/2022]
Abstract
Cancer cell metastasis is responsible for approximately 90% of deaths related to cancer. The migration of cancer cells away from the primary tumor and into healthy tissue is driven in part by contact guidance, or directed migration in response to aligned extracellular matrix. While contact guidance has been a focus of many studies, much of this research has explored environments that present 2D contact guidance structures. Contact guidance environments in 3D more closely resemble in vivo conditions and model cell-ECM interactions better than 2D environments. While most cells engage in directed migration on potent 2D contact guidance cues, there is diversity in response to contact guidance cues based on whether the cell migrates with a mesenchymal or amoeboid migration mode. In this paper, rotational alignment of collagen gels was used to study the differences in contact guidance between MDA-MB-231 (mesenchymal) and MTLn3 (amoeboid) cells. MDA-MB-231 cells migrate with high directional fidelity in aligned collagen gels, while MTLn3 cells show no directional migration. The collagen stiffness was increased through glycation, resulting in decreased MDA-MB-231 directionality in aligned collagen gels. Interestingly, partial inhibition of cell contractility dramatically decreased directionality in MDA-MB-231 cells. The directionality of MDA-MB-231 cells was most sensitive to ROCK inhibition, but unlike in 2D contact guidance environments, cell directionality and speed are more tightly coupled. Modulation of the contractile apparatus appears to more potently affect contact guidance than modulation of extracellular mechanical properties of the contact guidance cue. STATEMENT OF SIGNIFICANCE Collagen fiber alignment in the tumor microenvironment directs migration, a process called contact guidance, enhancing the efficiency of cancer invasion and metastasis. 3D systems that assess contact guidance by locally orienting collagen fiber alignment are lacking. Furthermore, cell type differences and the role of extracellular matrix stiffness in tuning contact guidance fidelity are not well characterized. In this paper rotational alignment of collagen fibers is used as a 3D contact guidance cue to illuminate cell type differences and the role of extracellular matrix stiffness in guiding cell migration along aligned fibers of collagen. This local alignment offers a simple approach by which to couple collagen alignment with gradients in other directional cues in devices such as microfluidic chambers.
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Affiliation(s)
- Jacob A M Nuhn
- Department of Chemical and Biological Engineering, Iowa State University, United States
| | - Anai M Perez
- Department of Chemistry and Physics, Grand View University, United States
| | - Ian C Schneider
- Department of Chemical and Biological Engineering, Iowa State University, United States; Department of Genetics, Development and Cell Biology, Iowa State University, United States.
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16
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Nam DH, Lee KB, Ge X. Functional Production of Catalytic Domains of Human MMPs in Escherichia coli Periplasm. Methods Mol Biol 2018; 1731:65-72. [PMID: 29318544 DOI: 10.1007/978-1-4939-7595-2_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Due to their central roles in tumor growth and invasion, milligram-level amounts of active MMPs are frequently required for cancer research and development of chemical or biological MMP inhibitors. Here we describe methods for functional production of catalytic domains of MMPs (cdMMPs) in E. coli periplasm without refolding or activation process. We demonstrate applications of this straightforward approach for cdMMP-9, cdMMP-14, and cdMMP-14 mutants.
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Affiliation(s)
- Dong Hyun Nam
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Ki Baek Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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17
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Abstract
Inhibiting individual MMPs of biomedical importance with high selectivity is critical for both fundamental research and therapy development. Here we describe the methods for discovery of inhibitory monoclonal antibodies from synthetic human antibody phage display libraries carrying convex paratopes encoded by long complementarity-determining region (CDR)-H3 segments. We demonstrate the application of this technique for isolation of highly specific and potent antibody inhibitors of human MMP-14.
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Affiliation(s)
- Dong Hyun Nam
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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