top of page

Publication Spotlights  

Active-site MMP-selective antibody inhibitors discovered from convex paratope synthetic libraries

Dong Hyun Nam, Carlos Rodriguez, Albert G. Remacle, Alex Y. Strongin, Xin Ge

PNAS 113: 14970-14975 (2016)


The matrix metalloproteinase (MMP) family members are promising drug targets in diversified pathologies. Clinical trial failures taught us that selective, rather than broad-specificity, inhibitors are required for successful MMP therapies. Achieving target selectivity with small-molecule MMP inhibitors, however, is exceedingly difficult. Because the antigen-binding sites in conventional antibodies are predominantly incompatible with the concave reaction pockets of MMPs, design of inhibitory antibodies, an attractive alternative for selective inhibition, is also challenging. We synthesized human antibody libraries encoding extended convex antigen-binding sites and isolated a panel of inhibitory Fabs that selectively and efficiently inhibited MMP-14, a promising drug target in cancer. The pipeline we established can now be readily applied for the generation of inhibitory antibodies targeting multiple additional enzymes besides MMPs alone.

Functional selection of protease inhibitory antibodies

Tyler Lopez, Zahid Mustafa, Chuan Chen, Ki Baek Lee, Aaron Ramirez, Chris Benitez, Xin Luo, Ru-Rong Ji, Xin Ge

PNAS 116: 16314-16319 (2019)


Proteases precisely control a wide variety of physiological processes and thus are important drug targets. Compared with small-molecule inhibitors, monoclonal antibodies (mAbs) are attractive, as they provide required specificity. However, finding inhibitory mAbs is often a bottleneck, largely due to lack of a function-based selection method. We overcame this obstacle and successfully isolated mAbs that effectively inhibited 5 therapeutic targets spanning 4 basic classes of proteases. Our mAb inhibitors are highly selective and deliver desired biochemical and biological actions, including reduction of amyloid beta formation in vitro and pain relief in animal behavioral tests. Thus, the technique described here can be readily applied to many pathophysiologically important proteases for the discovery and engineering of therapeutic mAbs.

High-Fidelity Large-Diversity Monoclonal Mammalian Cell Libraries by Cell Cycle Arrested Recombinase-Mediated Cassette Exchange (aRMCE)

Chuan Chen, Zening Wang, Minhyo Kang, Ki Baek Lee, Xin Ge

Nucleic Acid Res 51: e113 [2023]

Directed evolution is an effective way of protein engineering and typically performed in microbial systems. Although mammalian cells support protein folding, proper post-translational modifications, and cellular signaling all critical for studying mammalian biology and developing therapeutics, conducting directed evolution in mammalian cells is largely handicapped due to lack of a robust approach to construct high quality libraries. This study develops a platform technology that meets all desired criteria of an ideal library construction in mammalian cells – single variant per cell, accurate genomic integration, uniform transcription level, and large diversity. Besides demonstrated application of engineering antibody constant domains for enhanced immune response, the technology developed in this study has broad impacts for engineering proteins of biological functions that need mammalian environment. 


Selected Publications 

Wang Z, Chen C, Ge X. Large T antigen mediated donor gene replication improves site-specific recombination efficiency, Frontiers in Bioengineering Biotechnology [2024] 12:1377167. PMID: 38737535

Li Y, Ge X, Ji R-R. Pain Management by Chemogenetic Control of Sensory Neurons. Cell Report Medicine [2023] 4:101338. PMID: 38118411

Choe H, Antee T, Ge X. Substrate Derived Sequences Act as Subsite Blocking Motifs in Protease Inhibitory Antibodies. Protein Sciences [2023] 32[7]:e469. PMID: 37278099

Matsuoka Y, Furutani K, Lee KB, Ge X, Ji RR.: Inhibition of Diabetic Neuropathic Pain by Intrathecal and Intravenous Administration of MMP-9 Monoclonal Antibody in Mice. Journal of Pain [2023] 24[4]: 46. PMID: 38118411 

Kang M, Wang Z, Ge X. One-Step Production of Fully Biotinylated and Glycosylated Human Fc Gamma Receptors. Biotechnology Progress [2023] 40[1]:e3392. PMID: 37734055

Nam DH, Lee KB, Kruchowy E, Pham H, Ge X. Protease Inhibition Mechanism of Camelid-Like Synthetic Human Antibodies. Biochemistry (2020) 59[40]:3802-3812. PMID: 32997500

Lee KB, Dunn Z, Lopez T, Mustafa Z, Ge X. Generation of Highly Selective Monoclonal Antibodies Inhibiting a Recalcitrant Protease Using Decoy Designs. Biotechnology and Bioengineering (2020) 117[12]:3664-3676. PMID: 32716053

Li X, Zhao Y, Chen C, Lee H-H, Wang Z, Zhang N, Kolonin MG, An Z, Ge X, Scherer PE, Sun K. Critical Role of Matrix Metalloproteinase 14 in Adipose Tissue Remodeling during Obesity.

Molecular and Cellular Biology (2020) 40[8]:e00564-19. PMID: 31988105

Lee KB, Dunn Z, Ge X. Reducing Proteolytic Liability of a MMP‐14 Inhibitory Antibody by Site‐Saturation Mutagenesis. Protein Sciences (2019) 28[3]:643-653. PMID: 30592555

Lopez T, Ramirez A, Benitez C, Mustafa Z, Pham H, Sanchez R, Ge X. Selectivity Conversion of Protease Inhibitory Antibodies. Antibody Therapeutics (2018) 1[2]:55-63. PMID: 30406213

Lopez T, Chen C, Ramirez A, Chen KE, 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. Biotechnology and Bioengineering (2018) 115[11]:2673-2682. PMID: 30102763


Chen KE, Chen C, Radecki KC, Bustamante K, Lopez T, 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[50]:29431-29444. PMID: 30034628

Chen L, Holmes M, Schaefer E, Mulchandani A, Ge X. Highly Active Spore Biocatalyst by Self-Assembly of Co-Expressed Anchoring Scaffoldin and Multimeric Enzyme. Biotechnology and Bioengineering (2018) 115[3]:557-564. PMID: 29131302

Rodriguez C, Nam DH, Kruchowy E, Ge X. Efficient Antibody Assembly in E. coli Periplasm by Chaperone Co-expression and Culture Optimization. Applied Biochemistry and Biotechnology (2017) 183[2]:520-529. PMID: 28488120

Lee KB, Nam DH, Nuhn JA, Wang J, Schneider IC, Ge X. Direct Expression of Active Human Tissue Inhibitors of Metalloproteinases by Periplasmic Secretion in Escherichia coli. Microbial Cell Factories (2017) 16[1]:73. PMID: 28454584

Lopez T, Nam DH, Kaihara E, Mustafa Z, Ge X. Identification of Highly Selective MMP-14 Inhibitory Fabs by Deep Sequencing. Biotechnology and Bioengineering (2017) 114[6]:1140-1150. PMID: 28090632

Nam DH, Fang K, Rodriguez C, Lopez T, Ge X. Generation of Inhibitory Monoclonal Antibodies Targeting Membrane-Type 1 Matrix Metalloproteinase by Motif Grafting and CDR Optimization. Protein Engineering Design and Selection (2017) 30[2]:113-118. PMID: 27986919

Remacle AG, Cieplak P, Nam DH, Shiryaev SA, Ge X, Strongin AY. Selective Function-Blocking Monoclonal Human Antibody Highlights the Important Role of Membrane Type-1 Matrix Metalloproteinase (MT1-MMP) in Metastasis. Oncotarget (2017) 8:2781-2799. PMID: 27835863

Li XC, Wang C, Mulchandani A, Ge X. Engineering Soluble Human Paraoxonase 2 for Quorum Quenching. ACS Chemistry Biology (2016) 11[11]:3122-3131. PMID: 27623343

Nam DH, Ge X. Direct Production of Functional Matrix Metalloproteinase-14 Without Refolding or Activation and its Application for In Vitro Inhibition Assays. Biotechnology and Bioengineering (2016) 113[4]:717-723. PMID: 26416249

View full publication list at PubMed - My BibliographyGoogle Scholar


Ge X, Lopez T, Ji RR. MMP-9 Antibodies and Methods of Use Thereof. US62/851001. Licensed to Releviate Therapeutics

Ge X, Lee KB. Protease Inhibitory Antibodies and Method of Use Thereof. US11332546. Licensed to Maverick Therapeutics. 

Ge X, Nam DH, Lopez T. Inhibitory Antibodies and Methods of Use Thereof. US10975166; WO2018067198A1. Licensed to Releviate Therapeutics. 

Reddy ST, Ge X, Boutz D, Ellington AD, Marcotte EM, Georgiou G. Rapid Isolation of Monoclonal Antibodies from Animals. US9090674B2; EP2572203B1; KR20130135028A; CN103003697A; CA2799746A1; WO2011146514A3. Licensed to Cell Signaling Technology Inc.

Ge X, Mazor Y, Georgiou G. Methods for Creating Antibody Libraries. US12868399; EP2470653A1; CA2772298A1; WO2011025826A1.

Chilkoti A, Carlson KT, Christensen T, Filipe CDM, Ge X. Purification of Low-Abundant Recombinant Proteins from Cell Culture. WO2008024311A3. Licensed to PhaseBio Pharmaceuticals Inc. 

bottom of page