1
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Yamazaki T, Nagatoishi S, Yamawaki T, Nozawa T, Matsunaga R, Nakakido M, Caaveiro JMM, Nakagawa I, Tsumoto K. Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J Biol Chem 2023; 299:105254. [PMID: 37716701 PMCID: PMC10582769 DOI: 10.1016/j.jbc.2023.105254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Listeriosis, caused by infection with Listeria monocytogenes, is a severe disease with a high mortality rate. The L. monocytogenes virulence factor, internalin family protein InlA, which binds to the host receptor E-cadherin, is necessary to invade host cells. Here, we isolated two single-domain antibodies (VHHs) that bind to InlA with picomolar affinities from an alpaca immune library using the phage display method. These InlA-specific VHHs inhibited the binding of InlA to the extracellular domains of E-cadherin in vitro as shown by biophysical interaction analysis. Furthermore, we determined that the VHHs inhibited the invasion of L. monocytogenes into host cells in culture. High-resolution X-ray structure analyses of the complexes of VHHs with InlA revealed that the VHHs bind to the same binding site as E-cadherin against InlA. We conclude that these VHHs have the potential for use as drugs to treat listeriosis.
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Affiliation(s)
- Taichi Yamazaki
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Tsukushi Yamawaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takashi Nozawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jose M M Caaveiro
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
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2
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Senoo A, Nagatoishi S, Kuroda D, Ito S, Ueno G, Caaveiro JMM, Tsumoto K. Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion. Protein Sci 2023; 32:e4744. [PMID: 37531208 PMCID: PMC10443342 DOI: 10.1002/pro.4744] [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: 04/19/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
Small molecules that regulate protein-protein interactions can be valuable drugs; however, the development of such small molecules is challenging as the molecule must interfere with an interaction that often involves a large surface area. Herein, we propose that modulating the conformational ensemble of the proteins participating in a given interaction, rather than blocking the interaction by directly binding to the interface, is a relevant strategy for interfering with a protein-protein interaction. In this study, we applied this concept to P-cadherin, a cell surface protein forming homodimers that are essential for cell-cell adhesion in various biological contexts. We first determined the crystal structure of P-cadherin with a small molecule inhibitor whose inhibitory mechanism was unknown. Molecular dynamics simulations suggest that the inhibition of cell adhesion by this small molecule results from modulation of the conformational ensemble of P-cadherin. Our study demonstrates the potential of small molecules altering the conformation ensemble of a protein as inhibitors of biological relevant protein-protein interactions.
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Affiliation(s)
- Akinobu Senoo
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Department of Global Healthcare, Graduate School of Pharmaceutical SciencesKyushu UniversityFukuokaJapan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Research Center for Drug and Vaccine DevelopmentNational Institute of Infectious DiseasesTokyoJapan
| | - Sho Ito
- DIC Central Research LaboratoriesChibaJapan
| | - Go Ueno
- RIKEN SPring‐8 CenterSayo‐gunHyogoJapan
| | - Jose M. M. Caaveiro
- Department of Global Healthcare, Graduate School of Pharmaceutical SciencesKyushu UniversityFukuokaJapan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
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3
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Troyanovsky SM. Adherens junction: the ensemble of specialized cadherin clusters. Trends Cell Biol 2023; 33:374-387. [PMID: 36127186 PMCID: PMC10020127 DOI: 10.1016/j.tcb.2022.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022]
Abstract
The cell-cell connections in adherens junctions (AJs) are mediated by transmembrane receptors, type I cadherins (referred to here as cadherins). These cadherin-based connections (or trans bonds) are weak. To upregulate their strength, cadherins exploit avidity, the increased affinity of binding between cadherin clusters compared with isolated monomers. Formation of such clusters is a unique molecular process that is driven by a synergy of direct and indirect cis interactions between cadherins located at the same cell. In addition to their role in adhesion, cadherin clusters provide structural scaffolds for cytosolic proteins, which implicate cadherin into different cellular activities and signaling pathways. The cluster lifetime, which depends on the actin cytoskeleton, and on the mechanical forces it generates, determines the strength of AJs and their plasticity. The key aspects of cadherin adhesion, therefore, cannot be understood at the level of isolated cadherin molecules, but should be discussed in the context of cadherin clusters.
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Affiliation(s)
- Sergey M Troyanovsky
- Department of Dermatology, Northwestern University, The Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Cell and Molecular Biology, Northwestern University, The Feinberg School of Medicine, Chicago, IL 60611, USA.
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4
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Yui A, Kuroda D, Maruno T, Nakakido M, Nagatoishi S, Uchiyama S, Tsumoto K. Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene. Sci Rep 2023; 13:6493. [PMID: 37081068 PMCID: PMC10117238 DOI: 10.1038/s41598-023-32444-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/28/2023] [Indexed: 04/22/2023] Open
Abstract
LI-cadherin is a member of the cadherin superfamily. LI-cadherin mediates Ca2+-dependent cell-cell adhesion through homodimerization. A previous study reported two single nucleotide polymorphisms (SNPs) in the LI-cadherin-coding gene (CDH17). These SNPs correspond to the amino acid changes of Lys115 to Glu and Glu739 to Ala. Patients with colorectal cancer carrying these SNPs are reported to have a higher risk of lymph node metastasis than patients without the SNPs. Although proteins associated with metastasis have been identified, the molecular mechanisms underlying the functions of these proteins remain unclear, making it difficult to develop effective strategies to prevent metastasis. In this study, we employed biochemical assays and molecular dynamics (MD) simulations to elucidate the molecular mechanisms by which the amino acid changes caused by the SNPs in the LI-cadherin-coding gene increase the risk of metastasis. Cell aggregation assays showed that the amino acid changes weakened the LI-cadherin-dependent cell-cell adhesion. In vitro assays demonstrated a decrease in homodimerization tendency and MD simulations suggested an alteration in the intramolecular hydrogen bond network by the mutation of Lys115. Taken together, our results indicate that the increased risk of lymph node metastasis is due to weakened cell-cell adhesion caused by the decrease in homodimerization tendency.
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Affiliation(s)
- Anna Yui
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- U-Medico Inc., Osaka, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
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5
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Kingston RL, Millane RP. A general method for directly phasing diffraction data from high-solvent-content protein crystals. IUCRJ 2022; 9:648-665. [PMID: 36071801 PMCID: PMC9438493 DOI: 10.1107/s2052252522006996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60-0.85. The procedure works robustly at intermediate resolutions (1.9-3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70.
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Affiliation(s)
- Richard Lawrence Kingston
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland City, Auckland 1010, New Zealand
| | - Rick P. Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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6
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Maker A, Bolejack M, Schecterson L, Hammerson B, Abendroth J, Edwards TE, Staker B, Myler PJ, Gumbiner BM. Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography. PNAS NEXUS 2022; 1:pgac163. [PMID: 36157596 PMCID: PMC9491697 DOI: 10.1093/pnasnexus/pgac163] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/15/2022] [Indexed: 01/29/2023]
Abstract
E-cadherin adhesion is regulated at the cell surface, a process that can be replicated by activating antibodies. We use cryo-electron microscopy (EM) and X-ray crystallography to examine functional states of the cadherin adhesive dimer. This dimer is mediated by N-terminal beta strand-swapping involving Trp2, and forms via a different transient X-dimer intermediate. X-dimers are observed in cryo-EM along with monomers and strand-swap dimers, indicating that X-dimers form stable interactions. A novel EC4-mediated dimer was also observed. Activating Fab binding caused no gross structural changes in E-cadherin monomers, but can facilitate strand swapping. Moreover, activating Fab binding is incompatible with the formation of the X-dimer. Both cryo-EM and X-ray crystallography reveal a distinctive twisted strand-swap dimer conformation caused by an outward shift in the N-terminal beta strand that may represent a strengthened state. Thus, regulation of adhesion involves changes in cadherin dimer configurations.
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Affiliation(s)
- Allison Maker
- Department of Biochemistry, University of Washington, USA,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, USA
| | - Madison Bolejack
- UCB Pharma, Bainbridge, WA, USA,Seattle Structural Genomics Center for Infectious Disease, USA
| | - Leslayann Schecterson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, USA
| | - Brad Hammerson
- Seattle Structural Genomics Center for Infectious Disease, USA,Center for Global Infectious Disease Research, Seattle Children's Research Institute, USA
| | - Jan Abendroth
- UCB Pharma, Bainbridge, WA, USA,Seattle Structural Genomics Center for Infectious Disease, USA
| | - Thomas E Edwards
- UCB Pharma, Bainbridge, WA, USA,Seattle Structural Genomics Center for Infectious Disease, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, USA,Center for Global Infectious Disease Research, Seattle Children's Research Institute, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, USA,Center for Global Infectious Disease Research, Seattle Children's Research Institute, USA,Department of Pediatrics, University of Washington, USA,Department of Biomedical Informatics and Medical Education, University of Washington, USA
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7
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Multiple dimeric structures and strand-swap dimerization of E-cadherin in solution visualized by high-speed atomic force microscopy. Proc Natl Acad Sci U S A 2022; 119:e2208067119. [PMID: 35867820 PMCID: PMC9335211 DOI: 10.1073/pnas.2208067119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Classical cadherins play key roles in cell-cell adhesion. The adhesion process is thought to comprise mainly two steps: X-dimer and strand-swap (SS-) dimer formation of the extracellular domains (ectodomains) of cadherins. The dimerization mechanism of this two-step process has been investigated for type I cadherins, including E-cadherin, of classical cadherins, whereas other binding states also have been proposed, raising the possibility of additional binding processes required for the cadherin dimerization. However, technical limitations in observing single-molecule structures and their dynamics have precluded the investigation of the dynamic binding process of cadherin. Here, we used high-speed atomic force microscopy (HS-AFM) to observe full-length ectodomains of E-cadherin in solution and identified multiple dimeric structures that had not been reported previously. HS-AFM revealed that almost half of the cadherin dimers showed S- (or reverse S-) shaped conformations, which had more dynamic properties than the SS- and X-like dimers. The combined HS-AFM, mutational, and molecular modeling analyses showed that the S-shaped dimer was formed by membrane-distal ectodomains, while the binding interface was different from that of SS- and X-dimers. Furthermore, the formation of the SS-dimer from the S-shaped and X-like dimers was directly visualized, suggesting the processes of SS-dimer formation from S-shaped and X-dimers during cadherin dimerization.
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8
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Dash S, Duraivelan K, Hansda A, Kumari P, Chatterjee S, Mukherjee G, Samanta D. Heterophilic recognition between E-cadherin and N-cadherin relies on same canonical binding interface as required for E-cadherin homodimerization. Arch Biochem Biophys 2022; 727:109329. [PMID: 35738425 DOI: 10.1016/j.abb.2022.109329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 11/17/2022]
Abstract
Cadherins are a family of cell surface glycoproteins that mediate Ca2+-dependent cell to cell adhesion. They organize to form large macromolecular assemblies at the junctions of cells in order to form and maintain the integrity of tissue structures, thereby playing an indispensable role in the multicellular organization. Notably, a large body of research on E- and N-cadherin, the two most widely studied members of the cadherin superfamily, suggest for homophilic associations among them to drive cell adhesion. Interestingly, latest studies also highlight for direct crosstalk among these two classical cadherins to form heterotypic connections in physiological as well as in disease environment. However, the molecular details for the heterophilic association of E-cadherin and N-cadherin has not been investigated yet, which we aimed to address in this work. Using surface plasmon resonance and flow cytometry based biophysical studies we observed heterophilic interaction between E- and N-cadherin mediated through the membrane distal ectodomains. Further, the heterodimeric interface of E-cadherin and N-cadherin was mapped using structure-guided mutational studies followed by complementary biophysical analyses to identify the important interface residues involved in the interaction. The results obtained imply significant resemblance in the interface residues of E-cadherin that are crucial for homophilic recognition of E-cadherin and heterophilic recognition of N-cadherin as well.
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Affiliation(s)
- Sagarika Dash
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Kheerthana Duraivelan
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Anita Hansda
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Puja Kumari
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Shruti Chatterjee
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Gayatri Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal, 721302, India.
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9
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Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion. Commun Biol 2021; 4:1041. [PMID: 34493804 PMCID: PMC8423723 DOI: 10.1038/s42003-021-02575-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Many cadherin family proteins are associated with diseases such as cancer. Since cell adhesion requires homodimerization of cadherin molecules, a small-molecule regulator of dimerization would have therapeutic potential. Herein, we describe identification of a P-cadherin-specific chemical fragment that inhibits P-cadherin-mediated cell adhesion. Although the identified molecule is a fragment compound, it binds to a cavity of P-cadherin that has not previously been targeted, indirectly prevents formation of hydrogen bonds necessary for formation of an intermediate called the X dimer and thus modulates the process of X dimerization. Our findings will impact on a strategy for regulation of protein-protein interactions and stepwise assembly of protein complexes using small molecules.
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10
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Yui A, Caaveiro JMM, Kuroda D, Nakakido M, Nagatoishi S, Goda S, Maruno T, Uchiyama S, Tsumoto K. Mechanism of dimerization and structural features of human LI-cadherin. J Biol Chem 2021; 297:101054. [PMID: 34364873 PMCID: PMC8427231 DOI: 10.1016/j.jbc.2021.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/02/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Liver intestine (LI)-cadherin is a member of the cadherin superfamily, which encompasses a group of Ca2+-dependent cell-adhesion proteins. The expression of LI-cadherin is observed on various types of cells in the human body, such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-cadherin is a promising target for gastric cancer imaging. However, because the cell adhesion mechanism of LI-cadherin has remained unknown, rational design of therapeutic molecules targeting this cadherin has been hampered. Here, we have studied the homodimerization mechanism of LI-cadherin. We report the crystal structure of the LI-cadherin homodimer containing its first four extracellular cadherin repeats (EC1-4). The EC1-4 homodimer exhibited a unique architecture different from that of other cadherins reported so far, driven by the interactions between EC2 of one protein chain and EC4 of the second protein chain. The crystal structure also revealed that LI-cadherin possesses a noncanonical calcium ion-free linker between the EC2 and EC3 domains. Various biochemical techniques and molecular dynamics simulations were employed to elucidate the mechanism of homodimerization. We also showed that the formation of the homodimer observed in the crystal structure is necessary for LI-cadherin-dependent cell adhesion by performing cell aggregation assays. Taken together, our data provide structural insights necessary to advance the use of LI-cadherin as a target for imaging gastric cancer.
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Affiliation(s)
- Anna Yui
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Shuichiro Goda
- Graduate School of Science and Engineering, Soka University, Tokyo, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
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11
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Sheng Q, D'Alessio JA, Menezes DL, Karim C, Tang Y, Tam A, Clark S, Ying C, Connor A, Mansfield KG, Rondeau JM, Ghoddusi M, Geyer FC, Gu J, McLaughlin ME, Newcombe R, Elliot G, Tschantz WR, Lehmann S, Fanton CP, Miller K, Huber T, Rendahl KG, Jeffry U, Pryer NK, Lees E, Kwon P, Abraham JA, Damiano JS, Abrams TJ. PCA062, a P-cadherin Targeting Antibody-Drug Conjugate, Displays Potent Antitumor Activity Against P-cadherin-expressing Malignancies. Mol Cancer Ther 2021; 20:1270-1282. [PMID: 33879555 DOI: 10.1158/1535-7163.mct-20-0708] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/19/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022]
Abstract
The cell surface glycoprotein P-cadherin is highly expressed in a number of malignancies, including those arising in the epithelium of the bladder, breast, esophagus, lung, and upper aerodigestive system. PCA062 is a P-cadherin specific antibody-drug conjugate that utilizes the clinically validated SMCC-DM1 linker payload to mediate potent cytotoxicity in cell lines expressing high levels of P-cadherin in vitro, while displaying no specific activity in P-cadherin-negative cell lines. High cell surface P-cadherin is necessary, but not sufficient, to mediate PCA062 cytotoxicity. In vivo, PCA062 demonstrated high serum stability and a potent ability to induce mitotic arrest. In addition, PCA062 was efficacious in clinically relevant models of P-cadherin-expressing cancers, including breast, esophageal, and head and neck. Preclinical non-human primate toxicology studies demonstrated a favorable safety profile that supports clinical development. Genome-wide CRISPR screens reveal that expression of the multidrug-resistant gene ABCC1 and the lysosomal transporter SLC46A3 differentially impact tumor cell sensitivity to PCA062. The preclinical data presented here suggest that PCA062 may have clinical value for treating patients with multiple cancer types including basal-like breast cancer.
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Affiliation(s)
- Qing Sheng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Daniel L Menezes
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Christopher Karim
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Yan Tang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Angela Tam
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Suzanna Clark
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Chi Ying
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Anu Connor
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Keith G Mansfield
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Majid Ghoddusi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Felipe C Geyer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Jane Gu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Rick Newcombe
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - GiNell Elliot
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Sylvie Lehmann
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Christie P Fanton
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Kathy Miller
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Thomas Huber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Ursula Jeffry
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Nancy K Pryer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Emma Lees
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Paul Kwon
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Judith A Abraham
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Jason S Damiano
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Tinya J Abrams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
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12
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Terzoli S, Tiana G. Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential. J Phys Chem B 2020; 124:4079-4088. [PMID: 32336092 PMCID: PMC8007105 DOI: 10.1021/acs.jpcb.0c01671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Studying the conformations
involved in the dimerization of cadherins
is highly relevant to understand the development of tissues and its
failure, which is associated with tumors and metastases. Experimental
techniques, like X-ray crystallography, can usually report only the
most stable conformations, missing minority states that could nonetheless
be important for the recognition mechanism. Computer simulations could
be a valid complement to the experimental approach. However, standard
all-atom protein models in explicit solvent are computationally too
demanding to search thoroughly the conformational space of multiple
chains composed of several hundreds of amino acids. To reach this
goal, we resorted to a coarse-grained model in implicit solvent. The
standard problem with this kind of model is to find a realistic potential
to describe its interactions. We used coevolutionary information from
cadherin alignments, corrected by a statistical potential, to build
an interaction potential, which is agnostic about the experimental
conformations of the protein. Using this model, we explored the conformational
space of multichain systems and validated the results comparing with
experimental data. We identified dimeric conformations that are sequence
specific and that can be useful to rationalize the mechanism of recognition
between cadherins.
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Affiliation(s)
- Sara Terzoli
- Department of Physics and Center for Complexity and Biosystems, Universitá degli Studi di Milano and INFN, via Celoria 16, Milano 20133, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Universitá degli Studi di Milano and INFN, via Celoria 16, Milano 20133, Italy
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Senoo A, Nagatoishi S, Moberg A, Babol LN, Mitani T, Tashima T, Kudo S, Tsumoto K. Inhibition of homophilic dimerization and disruption of cell adhesion by P-cadherin-specific small molecules from SPR-based assays. Chem Commun (Camb) 2018; 54:5350-5353. [DOI: 10.1039/c8cc01964a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our SPR-based screening identified a compound which was able to inhibit cell adhesion mediated by homophilic dimerization of P-cadherin.
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Affiliation(s)
- Akinobu Senoo
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Satoru Nagatoishi
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Anna Moberg
- GE Healthcare Bio-sciences AB
- SE-751 84 Uppsala
- Sweden
| | | | - Tomoya Mitani
- Life Science Division
- GE Healthcare Japan
- Tokyo 169-0073
- Japan
| | - Takumi Tashima
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Shota Kudo
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
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14
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Mège RM, Ishiyama N. Integration of Cadherin Adhesion and Cytoskeleton at Adherens Junctions. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028738. [PMID: 28096263 DOI: 10.1101/cshperspect.a028738] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The cadherin-catenin adhesion complex is the key component of the intercellular adherens junction (AJ) that contributes both to tissue stability and dynamic cell movements in epithelial and nonepithelial tissues. The cadherin adhesion complex bridges neighboring cells and the actin-myosin cytoskeleton, and thereby contributes to mechanical coupling between cells which drives many morphogenetic events and tissue repair. Mechanotransduction at cadherin adhesions enables cells to sense, signal, and respond to physical changes in their environment. Central to this process is the dynamic link of the complex to actin filaments (F-actin), themselves structurally dynamic and subject to tension generated by myosin II motors. We discuss in this review recent breakthroughs in understanding molecular and cellular aspects of the organization of the core cadherin-catenin complex in adherens junctions, its association to F-actin, its mechanosensitive regulation, and dynamics.
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Affiliation(s)
- René Marc Mège
- Institut Jacques Monod (IJM), CNRS UMR 7592 and Université Paris Diderot, Paris, France
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, TMDT 4-902, Toronto, Ontario, Canada
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15
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Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin. Sci Rep 2017; 7:39518. [PMID: 28045038 PMCID: PMC5206748 DOI: 10.1038/srep39518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/24/2016] [Indexed: 12/04/2022] Open
Abstract
Human P-cadherin is a cell adhesion protein of the family of classical cadherins, the overexpression of which is correlated with poor prognosis in various types of cancer. Antibodies inhibiting cell-cell adhesion mediated by P-cadherin show clear therapeutic effect, although the mechanistic basis explaining their effectiveness is still unclear. Based on structural, physicochemical, and functional analyses, we have elucidated the molecular mechanism of disruption of cell adhesion by antibodies targeting human P-cadherin. Herein we have studied three different antibodies, TSP5, TSP7, and TSP11, each recognizing a different epitope on the surface of the cell-adhesive domain (EC1). Although all these three antibodies recognized human P-cadherin with high affinity, only TSP7 disrupted cell adhesion. Notably, we demonstrated that TSP7 abolishes cell adhesion by disabling the so-called X-dimer (a kinetic adhesive intermediate), in addition to disrupting the strand-swap dimer (the final thermodynamic state). The inhibition of the X-dimer was crucial for the overall inhibitory effect, raising the therapeutic value of a kinetic intermediary not only for preventing, but also for reversing, cell adhesion mediated by a member of the classical cadherin family. These findings should help to design more innovative and effective therapeutic solutions targeting human P-cadherin.
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