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Engineering of tissue inhibitor of metalloproteinases TIMP-1 for fine discrimination between closely related stromelysins MMP-3 and MMP-10

Raeeszadeh-Sarmazdeh, Maryam and Coban, Mathew and Mahajan, Shivansh and Hockla, Alexandra and Sankaran, Banumathi and Downey, Gregory P. and Radisky, Derek C. and Radisky, Evette S. (2022) Engineering of tissue inhibitor of metalloproteinases TIMP-1 for fine discrimination between closely related stromelysins MMP-3 and MMP-10. Journal of Biological Chemistry, 298 (3). Art. No. 101654. ISSN 0021-9258. PMCID PMC8902619. doi:10.1016/j.jbc.2022.101654. https://resolver.caltech.edu/CaltechAUTHORS:20220614-836707000

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Abstract

Matrix metalloproteinases (MMPs) have long been known as key drivers in the development and progression of diseases, including cancer and neurodegenerative, cardiovascular, and many other inflammatory and degenerative diseases, making them attractive potential drug targets. Engineering selective inhibitors based upon tissue inhibitors of metalloproteinases (TIMPs), endogenous human proteins that tightly yet nonspecifically bind to the family of MMPs, represents a promising new avenue for therapeutic development. Here, we used a counter-selective screening strategy for directed evolution of yeast-displayed human TIMP-1 to obtain TIMP-1 variants highly selective for the inhibition of MMP-3 in preference over MMP-10. As MMP-3 and MMP-10 are the most similar MMPs in sequence, structure, and function, our results thus clearly demonstrate the capability for engineering full-length TIMP proteins to be highly selective MMP inhibitors. We show using protein crystal structures and models of MMP-3-selective TIMP-1 variants bound to MMP-3 and counter-target MMP-10 how structural alterations within the N-terminal and C-terminal TIMP-1 domains create new favorable and selective interactions with MMP-3 and disrupt unique interactions with MMP-10. While our MMP-3-selective inhibitors may be of interest for future investigation in diseases where this enzyme drives pathology, our platform and screening strategy can be employed for developing selective inhibitors of additional MMPs implicated as therapeutic targets in disease.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.jbc.2022.101654DOIArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc8902619/PubMed CentralArticle
ORCID:
AuthorORCID
Coban, Mathew0000-0001-6396-6759
Radisky, Evette S.0000-0003-3121-109X
Additional Information:© 2022 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology Under a Creative Commons license - Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). Received 9 November 2021, Revised 21 January 2022, Available online 29 January 2022, Version of Record 5 March 2022. We thank Dr Laura Lewis-Tuffin in the Mayo Clinic cell sorting facility for assistance with FACS of TIMP-1 libraries. The ALS-ENABLE beamlines are supported in part by US National Institutes of Health grant P30 GM124169-01. The Advanced Light Source is a Department of Energy Office of Science User Facility under contract no. DE-AC02-05CH11231. Author contributions. M. R.-S. and E. S. R. conceptualization; M. R.-S. and E. S. R. methodology; M. R.-S., M. C., and E. S. R. validation; M. R.-S., M. C., B. S., and E. S. R. formal analysis; M. R.-S., M. C., S. M., A. H., and B. S. investigation; A. H., B. S., and E. S. R. resources; M. R.-S., M. C., and E. S. R. data curation; M. R.-S., M. C., and E. S. R. writing–original draft; M. R.-S., M. C., B. S., G. P. D., D. C. R., and E. S. R. writing–review & editing; M. R.-S. and E. S. R. visualization; M. R.-S., G. P. D., D. C. R., and E. S. R. supervision; M. R.-S. and E. S. R. project administration; G. P. D., D. C. R., and E. S. R. funding acquisition. This work was supported by US National Institutes of Health grants (R01 GM132100 and R01 CA258274 [to E. S. R.], R01 HL157424 [to G. P. D., D. C. R., and E. S. R.]) and US Department of Defense grant (grant no.: W81XWH-16-2-0030 [to G. P. D. and D. C. R.]). M. R.-S. is supported in part by National Institutes of Health grant (grant no.: P20 GM103650). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Data availability. The crystal structures of MMP-3cd–TIMP-1 variant complexes have been deposited in the PDB, www.rcsb.org (PDB IDs: 7S7L and 7S7M). This article contains supporting information. The authors declare that they have no conflicts of interest with the contents of this article.
Funders:
Funding AgencyGrant Number
NIHP30 GM124169-01
Department of Energy (DOE)DE-AC02-05CH11231
NIHR01 GM132100
NIHR01 CA258274
NIHR01 HL157424
Department of DefenseW81XWH-16-2-0030
NIHP20 GM103650
Subject Keywords:matrix metalloproteinase; MMP; tissue inhibitor of metalloproteinases; TIMP; protein engineering; yeast surface display; directed evolution; protease; protease inhibitor; crystal structure
Issue or Number:3
PubMed Central ID:PMC8902619
DOI:10.1016/j.jbc.2022.101654
Record Number:CaltechAUTHORS:20220614-836707000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220614-836707000
Official Citation:Maryam Raeeszadeh-Sarmazdeh, Mathew Coban, Shivansh Mahajan, Alexandra Hockla, Banumathi Sankaran, Gregory P. Downey, Derek C. Radisky, Evette S. Radisky, Engineering of tissue inhibitor of metalloproteinases TIMP-1 for fine discrimination between closely related stromelysins MMP-3 and MMP-10, Journal of Biological Chemistry, Volume 298, Issue 3, 2022, 101654, ISSN 0021-9258, https://doi.org/10.1016/j.jbc.2022.101654.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:115164
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:15 Jun 2022 18:05
Last Modified:15 Jun 2022 18:05

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