Ge Lab
Biopharmaceutical Discovery
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
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
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
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.
Monoclonal antibodies inhibiting MMP-9 activity alleviate peripheral neuropathy in diabetic mice
Ki Baek Lee, Wei He, Yutaka Matsuoka, Sangsu Bang, Sushma Krishnan, Jing Xu, Qin Zhang, Letao Ma, Weiyuan Hu, Xiang Ao, Marc Parisien, Luda Diatchenko, Xinli Liu, Ru-Rong Ji, Xin Ge
Diabetic peripheral neuropathy (DPN) is a debilitating medical condition that affects millions of individuals, causing neuropathic pain and chronic wounds. Despite its substantial impact, there are currently no effective disease-modifying treatments available to prevent or reverse the progression of nerve damage. By regulating neuroinflammation, matrix metalloproteinase-9 (MMP-9) is both sufficient and required for the pathogenesis of neuropathy, representing a promising drug target for DPN; however, small-molecule inhibitors often lack target specificity. We developed a panel of selective, potent, and proteolytically stable monoclonal antibodies (mAbs) that inhibit MMP-9 activity as a treatment for DPN. We found that systematic administration of MMP-9 inhibitory mAbs alleviated mechanical and cold pain symptoms in diabetic mouse models and restored hind paw wound healing in diabetic mice. MMP-9 mAbs also reduced epidermal nerve fiber degeneration in diabetic mice by enhancing nerve mitochondrial function and promoting skin angiogenesis. Furthermore, we determined that MMP-9 expression in human dorsal root ganglia is increased among patients with diabetes, and human genetic analysis revealed that both rare coding of MMP9 and its common variants are associated with neuropathic pain phenotypes. Together, these translational findings indicate that MMP-9–specific mAbs hold potential as disease-modifying therapies for peripheral neuropathy and for reducing lower extremity complications associated with diabetes.
Selected Publications
Lee KB, He W, Matsuoka Y, Bang S, Krishnan S, Xu J, Zhang Q, Ma L, Hu W, Ao X, Parisien M, Diatchenko L, Liu X, Ji RR, Ge X. Monoclonal antibodies inhibiting MMP-9 activity alleviate peripheral neuropathy in diabetic mice. Science Translational Medicine (2026) 18(866):eadw3558. PMID: 42715343
Sarkar A, Michael S, Wang Z, Ge X. AlphaFold 3 prediction of TCR mimic Fv - pMHC complex structures and their validation and optimization. mAbs (2026) 18[1]:2719263. PMID: 42619491
Lee KB, Lee S, Reddi B, Krishnan S, Wang Z, Ge X. Achieving protease substrate-specific inhibition by mAb dual functional selections. Protein Science (2026) 35[7]:e70688. PMID: 42321978
Wang Z, Chen C, Ebrahimpour A, Kang M, Ge X. Fc Engineering by Monoclonal Mammalian Cell Display for Improved Affinity and Selectivity Towards FcrRs. Antibody Therapeutics (2024) 7:209–220. PMID: 39036072
Wang Z, Chen C, Ge X. Large T antigen mediated donor gene replication improves site-specific recombination efficiency. Frontier Bioengineering Biotechnology (2024) 12:1377167. PMID: 38737535
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
Chen C, Wang Z, Kang M, Lee KB, Ge X. High-Fidelity Large-Diversity Monoclonal Mammalian Cell Libraries by Cell Cycle Arrested Recombinase-Mediated Cassette Exchange (aRMCE). Nucleic Acid Research (2023) 51:e113. PMID: 37941133
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
Lopez T, Mustafa Z, Chen C, Lee KB, Ramirez A, Benitez C, Luo X, Ji R-R, Ge X. Functional Selection of Protease Inhibitory Antibodies. PNAS (2019) 116 [33]:16314–16319. PMID: 31363054
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 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
Chen L, Mulchandani A, Ge X. Spore-Displayed Enzyme Cascade with Tunable Stoichiometry. Biotechnology Progress (2017) 33[2]:383–389. PMID: 27977916
Nam DH, Rodriguez C, Remacle AG, Strongin AY, Ge X. Active-Site MMP-Selective Antibody Inhibitors Discovered from Convex Paratope Synthetic Libraries. PNAS (2016) 113[52]:14970–14975. PMID: 27965386
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 Google Scholar, OCRID, NCBI My Bibliography
Patents
Ge X, Ji RR, Lee KB, He W. Antibodies against MMP-9 and methods of use thereof. US provisional application 64/083,669.
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.