1
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Gorantla KR, Krishnan A, Waheed SO, Varghese A, DiCastri I, LaRouche C, Paik M, Fields GB, Karabencheva-Christova TG. Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1. Biochemistry 2024; 63:1925-1940. [PMID: 38963231 DOI: 10.1021/acs.biochem.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Anandhu Krishnan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Isabella DiCastri
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Meredith Paik
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Gregg B Fields
- Department of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458, United States
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2
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Radisky ES. Extracellular proteolysis in cancer: Proteases, substrates, and mechanisms in tumor progression and metastasis. J Biol Chem 2024; 300:107347. [PMID: 38718867 PMCID: PMC11170211 DOI: 10.1016/j.jbc.2024.107347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
A vast ensemble of extracellular proteins influences the development and progression of cancer, shaped and reshaped by a complex network of extracellular proteases. These proteases, belonging to the distinct classes of metalloproteases, serine proteases, cysteine proteases, and aspartic proteases, play a critical role in cancer. They often become dysregulated in cancer, with increases in pathological protease activity frequently driven by the loss of normal latency controls, diminished regulation by endogenous protease inhibitors, and changes in localization. Dysregulated proteases accelerate tumor progression and metastasis by degrading protein barriers within the extracellular matrix (ECM), stimulating tumor growth, reactivating dormant tumor cells, facilitating tumor cell escape from immune surveillance, and shifting stromal cells toward cancer-promoting behaviors through the precise proteolysis of specific substrates to alter their functions. These crucial substrates include ECM proteins and proteoglycans, soluble proteins secreted by tumor and stromal cells, and extracellular domains of cell surface proteins, including membrane receptors and adhesion proteins. The complexity of the extracellular protease web presents a significant challenge to untangle. Nevertheless, technological strides in proteomics, chemical biology, and the development of new probes and reagents are enabling progress and advancing our understanding of the pivotal importance of extracellular proteolysis in cancer.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA.
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3
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Abiola J, Berg AM, Aiyelaagbe O, Adeyi A, König S. Dabsylated Bradykinin Is Cleaved by Snake Venom Proteases from Echis ocellatus. Biomedicines 2024; 12:1027. [PMID: 38790989 PMCID: PMC11118064 DOI: 10.3390/biomedicines12051027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
The vasoactive peptide bradykinin (BK) is an important member of the renin-angiotensin system. Its discovery is tightly interwoven with snake venom research, because it was first detected in plasma following the addition of viper venom. While the fact that venoms liberate BK from a serum globulin fraction is well described, its destruction by the venom has largely gone unnoticed. Here, BK was found to be cleaved by snake venom metalloproteinases in the venom of Echis ocellatus, one of the deadliest snakes, which degraded its dabsylated form (DBK) in a few minutes after Pro7 (RPPGFSP↓FR). This is a common cleavage site for several mammalian proteases such as ACE, but is not typical for matrix metalloproteinases. Residual protease activity < 5% after addition of EDTA indicated that DBK is also cleaved by serine proteases to a minor extent. Mass spectrometry-based protein analysis provided spectral proof for several peptides of zinc metalloproteinase-disintegrin-like Eoc1, disintegrin EO4A, and three serine proteases in the venom.
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Affiliation(s)
- Julius Abiola
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
- Organic Unit, Department of Chemistry, University of Ibadan, Ibadan 200005, Nigeria
| | - Anna Maria Berg
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
| | - Olapeju Aiyelaagbe
- Organic Unit, Department of Chemistry, University of Ibadan, Ibadan 200005, Nigeria
| | - Akindele Adeyi
- Animal Physiology Unit, Department of Zoology, University of Ibadan, Ibadan 200005, Nigeria
| | - Simone König
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
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4
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Tian X, Feng M, Wei X, Cheng C, He K, Jiang T, He B, Gu Z. In situ formed depot of elastin-like polypeptide-hirudin fusion protein for long-acting antithrombotic therapy. Proc Natl Acad Sci U S A 2024; 121:e2314349121. [PMID: 38442174 PMCID: PMC10945803 DOI: 10.1073/pnas.2314349121] [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: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
Thrombosis, induced by abnormal coagulation or fibrinolytic systems, is the most common pathology associated with many life-threatening cardio-cerebrovascular diseases. However, first-line anticoagulant drugs suffer from rapid drug elimination and risk of hemorrhagic complications. Here, we developed an in situ formed depot of elastin-like polypeptide (ELP)-hirudin fusion protein with a prodrug-like feature for long-term antithrombotic therapy. Highly secretory expression of the fusion protein was achieved with the assistance of the Ffu312 tag. Integration of hirudin, ELP, and responsive moiety can customize fusion proteins with properties of adjustable in vivo retention and controllable recovery of drug bioactivity. After subcutaneous injection, the fusion protein can form a reservoir through temperature-induced coacervation of ELP and slowly diffuse into the blood circulation. The biological activity of hirudin is shielded due to the N-terminal modification, while the activated key proteases upon thrombus occurrence trigger the cleavage of fusion protein together with the release of hirudin, which has antithrombotic activity to counteract thrombosis. We substantiated that the optimized fusion protein produced long-term antithrombotic effects without the risk of bleeding in multiple animal thrombosis models.
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Affiliation(s)
- Xue Tian
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing211816, China
| | - Mingxing Feng
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing211816, China
| | - Xinwei Wei
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Cheng Cheng
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing211816, China
| | - Kaixin He
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Tianyue Jiang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing211816, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing211816, China
| | - Zhen Gu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
- Jinhua Institute of Zhejiang University, Jinhua321299, China
- Department of General Surgery, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Liangzhu Laboratory, Hangzhou311121, China
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5
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Xu S, Xu X, Wang Z, Wu R. A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability. Angew Chem Int Ed Engl 2024; 63:e202315286. [PMID: 38117010 PMCID: PMC10981938 DOI: 10.1002/anie.202315286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
The N-termini of proteins can regulate their degradation, and the same protein with different N-termini may have distinct dynamics. Recently, it was found that N-terminal glycine can serve as a degron recognized by two E3 ligases, but N-terminal glycine was also reported to stabilize proteins. Here we developed a chemoenzymatic method for selective enrichment of proteoforms with N-terminal glycine and integrated dual protease cleavage to further improve the enrichment specificity. Over 2000 unique peptides with protein N-terminal glycine were analyzed from >1000 proteins, and most of them are previously unknown, indicating the effectiveness of the current method to capture low-abundance proteoforms with N-terminal glycine. The degradation rates of proteoforms with N-terminal glycine were quantified along with those of proteins from the whole proteome. Bioinformatic analyses reveal that proteoforms with N-terminal glycine with the fastest and slowest degradation rates have different functions and localizations. Membrane proteins with N-terminal glycine and proteins with N-terminal glycine from the N-terminal methionine excision degrade more rapidly. Furthermore, the secondary structures, adjacent amino acid residues, and protease specificities for N-terminal glycine are also vital for protein degradation. The results advance our understanding of the effects of N-terminal glycine on protein properties and functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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6
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Romov IM, Nowzari RA, Page CP, Benes MR, Borzok MA, Wright NT. Prevention of Protease-Induced Degradation of Desmoplakin via Small Molecule Binding. J Pers Med 2024; 14:163. [PMID: 38392596 PMCID: PMC10890502 DOI: 10.3390/jpm14020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Desmoplakin (DSP) is a large (~260 kDa) protein found in the desmosome, the subcellular structure that links the intermediate filament network of one cell to its neighbor. A mutation "hot-spot" within the NH2-terminal of the DSP protein (residues 299-515) is associated with arrhythmogenic cardiomyopathy. In a subset of DSP variants, disease is linked to calpain hypersensitivity. Previous studies show that calpain hypersensitivity can be corrected in vitro through the addition of a bulky residue neighboring the cleavage site, suggesting that physically blocking calpain accessibility is a viable strategy to restore DSP levels. Here, we aim to find drug-like molecules that also block calpain-dependent degradation of DSP. To do this, we screened ~2500 small molecules to identify compounds that specifically rescue DSP protein levels in the presence of proteases. We find that several molecules, including sodium dodecyl sulfate, palmitoylethanolamide, GW0742, salirasib, eprosarten mesylate, and GSK1838705A prevent wildtype and disease-variant-carrying DSP protein degradation in the presence of both trypsin and calpain without altering protease function. Computational screenings did not predict which molecules would protect DSP, likely due to a lack of specific DSP-drug interactions. Molecular dynamic simulations of DSP-drug complexes suggest that some long hydrophobic molecules can bind in a shallow hydrophobic groove that runs alongside the protease cleavage site. Identification of these compounds lays the groundwork for pharmacological treatment for individuals harboring these hypersensitive DSP variants.
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Affiliation(s)
- Isabel M Romov
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Roujon A Nowzari
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Clay P Page
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Madeleine R Benes
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Maegen A Borzok
- Department of Biochemistry, Chemistry, Engineering and Physics, Commonwealth University of Pennsylvania, Mansfield, PA 16933, USA
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
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7
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Coates-Park S, Lazaroff C, Gurung S, Rich J, Colladay A, O’Neill M, Butler GS, Overall CM, Stetler-Stevenson WG, Peeney D. Tissue inhibitors of metalloproteinases are proteolytic targets of matrix metalloproteinase 9. Matrix Biol 2023; 123:59-70. [PMID: 37804930 PMCID: PMC10843048 DOI: 10.1016/j.matbio.2023.09.002] [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: 07/13/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023]
Abstract
Extracellular proteolysis and turnover are core processes of tissue homeostasis. The predominant matrix-degrading enzymes are members of the Matrix Metalloproteinase (MMP) family. MMPs extensively degrade core matrix components in addition to processing a range of other factors in the extracellular, plasma membrane, and intracellular compartments. The proteolytic activity of MMPs is modulated by the Tissue Inhibitors of Metalloproteinases (TIMPs), a family of four multi-functional matrisome proteins with extensively characterized MMP inhibitory functions. Thus, a well-regulated balance between MMP activity and TIMP levels has been described as critical for healthy tissue homeostasis, and this balance can be chronically disturbed in pathological processes. The relationship between MMPs and TIMPs is complex and lacks the constraints of a typical enzyme-inhibitor relationship due to secondary interactions between various MMPs (specifically gelatinases) and TIMP family members. We illustrate a new complexity in this system by describing how MMP9 can cleave members of the TIMP family when in molar excess. Proteolytic processing of TIMPs can generate functionally altered peptides with potentially novel attributes. We demonstrate here that all TIMPs are cleaved at their C-terminal tails by a molar excess of MMP9. This processing removes the N-glycosylation site for TIMP3 and prevents the TIMP2 interaction with latent proMMP2, a prerequisite for cell surface MMP14-mediated activation of proMMP2. TIMP2/4 are further cleaved producing ∼14 kDa N-terminal proteins linked to a smaller C-terminal domain through residual disulfide bridges. These cleaved TIMP2/4 complexes show perturbed MMP inhibitory activity, illustrating that MMP9 may bear a particularly prominent influence upon the TIMP:MMP balance in tissues.
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Affiliation(s)
- Sasha Coates-Park
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Carolyn Lazaroff
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
- Washington University in St. Louis School of Medicine, Department of Orthopedics
| | - Sadeechya Gurung
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Josh Rich
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Alexandra Colladay
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Maura O’Neill
- Protein Characterization Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Georgina S. Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Oral Biological and Medical Science, Faculty of Dentistry, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
| | - Christopher M. Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Oral Biological and Medical Science, Faculty of Dentistry, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
| | - William G. Stetler-Stevenson
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - David Peeney
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
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8
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Son J, Parveen S, MacPherson D, Marciano Y, Huang RH, Ulijn RV. MMP-responsive nanomaterials. Biomater Sci 2023; 11:6457-6479. [PMID: 37623747 DOI: 10.1039/d3bm00840a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Matrix metalloproteinases (MMP) are enzymes that degrade the extracellular matrix and regulate essential normal cell behaviors. Inhibition of these enzymes has been a strategy for anti-cancer therapy since the 1990s, but with limited success. A new type of MMP-targeting strategy exploits the innate selective hydrolytic activity and consequent catalytic signal amplification of the proteinases, rather than inhibiting it. Using nanomaterials, the enzymatic chemical reaction can trigger the temporal and spatial activation of the anti-cancer effects, amplify the associated response, and cause mechanical damage or report on cancer cells. We analyzed nearly 60 literature studies that incorporate chemical design strategies that lead to spatial, temporal, and mechanical control of the anti-cancer effect through four modes of action: nanomaterial shrinkage, induced aggregation, formation of cytotoxic nanofibers, and activation by de-PEGylation. From the literature analysis, we derived chemical design guidelines to control and enhance MMP activation of nanomaterials of various chemical compositions (peptide, lipid, polymer, inorganic). Finally, the review includes a guide on how multiple characteristics of the nanomaterial, such as substrate modification, supramolecular structure, and electrostatic charge should be collectively considered for the targeted MMP to result in optimal kinetics of enzyme action on the nanomaterial, which allow access to amplification and additional levels of spatial, temporal, and mechanical control of the response. Although this review focuses on the design strategies of MMP-responsive nanomaterials in cancer applications, these guidelines are expected to be generalizable to systems that target MMP for treatment or detection of cancer and other diseases, as well as other enzyme-responsive nanomaterials.
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Affiliation(s)
- Jiye Son
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York (CUNY), 85 Saint Nicholas Terrace, New York, NY 10031, USA.
| | - Sadiyah Parveen
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York (CUNY), 85 Saint Nicholas Terrace, New York, NY 10031, USA.
- Department of Biomedical Engineering, The City College of New York, CUNY, 160 Convent Avenue, New York, NY 10031, USA
| | - Douglas MacPherson
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York (CUNY), 85 Saint Nicholas Terrace, New York, NY 10031, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of CUNY, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
- Department of Chemistry, Brooklyn College, CUNY, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Yaron Marciano
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York (CUNY), 85 Saint Nicholas Terrace, New York, NY 10031, USA.
- Department of Chemistry, Brooklyn College, CUNY, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Richard H Huang
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York (CUNY), 85 Saint Nicholas Terrace, New York, NY 10031, USA.
| | - Rein V Ulijn
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York (CUNY), 85 Saint Nicholas Terrace, New York, NY 10031, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of CUNY, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Chemistry, The Graduate Center of CUNY, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, CUNY, 695 Park Avenue, New York, NY 10065, USA
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9
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Matveev EV, Safronov VV, Ponomarev GV, Kazanov MD. Predicting Structural Susceptibility of Proteins to Proteolytic Processing. Int J Mol Sci 2023; 24:10761. [PMID: 37445939 DOI: 10.3390/ijms241310761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The importance of 3D protein structure in proteolytic processing is well known. However, despite the plethora of existing methods for predicting proteolytic sites, only a few of them utilize the structural features of potential substrates as predictors. Moreover, to our knowledge, there is currently no method available for predicting the structural susceptibility of protein regions to proteolysis. We developed such a method using data from CutDB, a database that contains experimentally verified proteolytic events. For prediction, we utilized structural features that have been shown to influence proteolysis in earlier studies, such as solvent accessibility, secondary structure, and temperature factor. Additionally, we introduced new structural features, including length of protruded loops and flexibility of protein termini. To maximize the prediction quality of the method, we carefully curated the training set, selected an appropriate machine learning method, and sampled negative examples to determine the optimal positive-to-negative class size ratio. We demonstrated that combining our method with models of protease primary specificity can outperform existing bioinformatics methods for the prediction of proteolytic sites. We also discussed the possibility of utilizing this method for bioinformatics prediction of other post-translational modifications.
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Affiliation(s)
- Evgenii V Matveev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117998, Russia
| | - Vyacheslav V Safronov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Gennady V Ponomarev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Marat D Kazanov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117998, Russia
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
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10
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Choi JY, Chung E. Molecular Dynamics Simulations of Matrix Metalloproteinase 13 and the Analysis of the Specificity Loop and the S1'-Site. Int J Mol Sci 2023; 24:10577. [PMID: 37445757 PMCID: PMC10342107 DOI: 10.3390/ijms241310577] [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: 04/01/2023] [Revised: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
The specificity loop of Matrix Metalloproteinases (MMPs) is known to regulate recognition of their substrates, and the S1'-site surrounded by the loop is a unique place to address the selectivity of ligands toward each MMP. Molecular dynamics (MD) simulations of apo-MMP-13 and its complex forms with various ligands were conducted to identify the role of the specificity loop for the ligand binding to MMP-13. The MD simulations showed the dual role of T247 as a hydrogen bond donor to the ligand, as well as a contributor to the formation of the van der Waal surface area, with T245 and K249 on the S1'-site. The hydrophobic surface area mediated by T247 blocks the access of water molecules to the S1'-site of MMP-13 and stabilizes the ligand in the site. The F252 residue is flexible in order to search for the optimum location in the S1'-site of the apo-MMP-13, but once a ligand binds to the S1'-site, it can form offset π-π or edge-to-π stacking interactions with the ligand. Lastly, H222 and Y244 provide the offset π-π and π-CH(Cβ) interactions on each side of the phenyl ring of the ligand, and this sandwiched interaction could be critical for the ligand binding to MMP-13.
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Affiliation(s)
- Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, Flushing, NY 11367, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Eugene Chung
- Department of Chemistry and Biochemistry, Queens College, Flushing, NY 11367, USA
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11
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Cui M, Nguyen D, Gaillez MP, Heiden S, Lin W, Thompson M, Reddavide FV, Chen Q, Zhang Y. Trio-pharmacophore DNA-encoded chemical library for simultaneous selection of fragments and linkers. Nat Commun 2023; 14:1481. [PMID: 36932079 PMCID: PMC10023787 DOI: 10.1038/s41467-023-37071-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The split-and-pool method has been widely used to synthesize chemical libraries of a large size for early drug discovery, albeit without the possibility of meaningful quality control. In contrast, a self-assembled DNA-encoded chemical library (DEL) allows us to construct an m x n-member library by mixing an m-member and an n-member pre-purified sub-library. Herein, we report a trio-pharmacophore DEL (T-DEL) of m x l x n members through assembling three pre-purified and validated sub-libraries. The middle sub-library is synthesized using DNA-templated synthesis with different reaction mechanisms and designed as a linkage connecting the fragments displayed on the flanking two sub-libraries. Despite assembling three fragments, the resulting compounds do not exceed the up-to-date standard of molecular weight regarding drug-likeness. We demonstrate the utility of T-DEL in linker optimization for known binding fragments against trypsin and carbonic anhydrase II and by de novo selections against matrix metalloprotease-2 and -9.
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Affiliation(s)
- Meiying Cui
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Michelle Patino Gaillez
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Weilin Lin
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | | | - Qinchang Chen
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, China.
- School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yixin Zhang
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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12
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Raj S, Unsworth LD. Targeting active sites of inflammation using inherent properties of tissue-resident mast cells. Acta Biomater 2023; 159:21-37. [PMID: 36657696 DOI: 10.1016/j.actbio.2023.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/12/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Mast cells play a pivotal role in initiating and directing host's immune response. They reside in tissues that primarily interface with the external environment. Activated mast cells respond to environmental cues throughout acute and chronic inflammation through releasing immune mediators via rapid degranulation, or long-term de novo expression. Mast cell activation results in the rapid release of a variety of unique enzymes and reactive oxygen species. Furthermore, the increased density of mast cell unique receptors like mas related G protein-coupled receptor X2 also characterizes the inflamed tissues. The presence of these molecules (either released mediators or surface receptors) are particular to the sites of active inflammation, and are a result of mast cell activation. Herein, the molecular design principles for capitalizing on these novel mast cell properties is discussed with the goal of manipulating localized inflammation. STATEMENT OF SIGNIFICANCE: Mast cells are immune regulating cells that play a crucial role in both innate and adaptive immune responses. The activation of mast cells causes the release of multiple unique profiles of biomolecules, which are specific to both tissue and disease. These unique characteristics are tightly regulated and afford a localized stimulus for targeting inflammatory diseases. Herein, these important mast cell attributes are discussed in the frame of highlighting strategies for the design of bioresponsive functional materials to target regions of inflammations.
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Affiliation(s)
- Shammy Raj
- Department of Chemical and Materials Engineering, Donadeo Innovation Centre for Engineering, 9211-116 Street NW, University of Alberta, Edmonton, AB, T6G1H9, Canada
| | - Larry D Unsworth
- Department of Chemical and Materials Engineering, Donadeo Innovation Centre for Engineering, 9211-116 Street NW, University of Alberta, Edmonton, AB, T6G1H9, Canada.
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13
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Kennedy EN, Foster CA, Barr SA, Bourret RB. General strategies for using amino acid sequence data to guide biochemical investigation of protein function. Biochem Soc Trans 2022; 50:1847-1858. [PMID: 36416676 PMCID: PMC10257402 DOI: 10.1042/bst20220849] [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: 08/18/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
The rapid increase of '-omics' data warrants the reconsideration of experimental strategies to investigate general protein function. Studying individual members of a protein family is likely insufficient to provide a complete mechanistic understanding of family functions, especially for diverse families with thousands of known members. Strategies that exploit large amounts of available amino acid sequence data can inspire and guide biochemical experiments, generating broadly applicable insights into a given family. Here we review several methods that utilize abundant sequence data to focus experimental efforts and identify features truly representative of a protein family or domain. First, coevolutionary relationships between residues within primary sequences can be successfully exploited to identify structurally and/or functionally important positions for experimental investigation. Second, functionally important variable residue positions typically occupy a limited sequence space, a property useful for guiding biochemical characterization of the effects of the most physiologically and evolutionarily relevant amino acids. Third, amino acid sequence variation within domains shared between different protein families can be used to sort a particular domain into multiple subtypes, inspiring further experimental designs. Although generally applicable to any kind of protein domain because they depend solely on amino acid sequences, the second and third approaches are reviewed in detail because they appear to have been used infrequently and offer immediate opportunities for new advances. Finally, we speculate that future technologies capable of analyzing and manipulating conserved and variable aspects of the three-dimensional structures of a protein family could lead to broad insights not attainable by current methods.
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Affiliation(s)
- Emily N. Kennedy
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Clay A. Foster
- Department of Pediatrics, Section Hematology/Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Sarah A. Barr
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Robert B. Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
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14
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Ćwilichowska N, Świderska KW, Dobrzyń A, Drąg M, Poręba M. Diagnostic and therapeutic potential of protease inhibition. Mol Aspects Med 2022; 88:101144. [PMID: 36174281 DOI: 10.1016/j.mam.2022.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Proteases are enzymes that hydrolyze peptide bonds in proteins and peptides; thus, they control virtually all biological processes. Our understanding of protease function has advanced considerably from nonselective digestive enzymes to highly specialized molecular scissors that orchestrate complex signaling networks through a limited proteolysis. The catalytic activity of proteases is tightly regulated at several levels, ranging from gene expression through trafficking and maturation to posttranslational modifications. However, when this delicate balance is disturbed, many diseases develop, including cancer, inflammatory disorders, diabetes, and neurodegenerative diseases. This new understanding of the role of proteases in pathologic physiology indicates that these enzymes represent excellent molecular targets for the development of therapeutic inhibitors, as well as for the design of chemical probes to visualize their redundant activity. Recently, numerous platform technologies have been developed to identify and optimize protease substrates and inhibitors, which were further used as lead structures for the development of chemical probes and therapeutic drugs. Due to this considerable success, the clinical potential of proteases in therapeutics and diagnostics is rapidly growing and is still not completely explored. Therefore, small molecules that can selectively target aberrant protease activity are emerging in diseases cells. In this review, we describe modern trends in the design of protease drugs as well as small molecule activity-based probes to visualize selected proteases in clinical settings.
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Affiliation(s)
- Natalia Ćwilichowska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina W Świderska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Dobrzyń
- Nencki Institute of Experimental Biology, Ludwika Pasteura 3, 02-093, Warsaw, Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
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15
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Austin MJ, Schunk H, Watkins C, Ling N, Chauvin J, Morton L, Rosales AM. Fluorescent Peptomer Substrates for Differential Degradation by Metalloproteases. Biomacromolecules 2022; 23:4909-4923. [PMID: 36269900 DOI: 10.1021/acs.biomac.2c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for an MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side-chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well tolerated in the P3 and P3' substrate sites and that the identity of the peptoid in these sites displays a moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with side-chain identity than side-chain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as "fingerprints" for the proteases and yielded separation by multivariate data analysis. To further demonstrate the practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.
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Affiliation(s)
- Mariah J Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Hattie Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Carolyn Watkins
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Natalie Ling
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Jeremy Chauvin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Logan Morton
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
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16
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Kim MH, Lim SH. Matrix Metalloproteinases and Glaucoma. Biomolecules 2022; 12:biom12101368. [PMID: 36291577 PMCID: PMC9599265 DOI: 10.3390/biom12101368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/19/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are enzymes that decompose extracellular matrix (ECM) proteins. MMPs are thought to play important roles in cellular processes, such as cell proliferation, differentiation, angiogenesis, migration, apoptosis, and host defense. MMPs are distributed in almost all intraocular tissues and are involved in physiological and pathological mechanisms of the eye. MMPs are also associated with glaucoma, a progressive neurodegenerative disease of the eyes. MMP activity affects intraocular pressure control and apoptosis of retinal ganglion cells, which are the pathological mechanisms of glaucoma. It also affects the risk of glaucoma development based on genetic pleomorphism. In addition, MMPs may affect the treatment outcomes of glaucoma, including the success rate of surgical treatment and side effects on the ocular surface due to glaucoma medications. This review discusses the various relationships between MMP and glaucoma.
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Affiliation(s)
- Moo Hyun Kim
- Department of Ophthalmology, Daegu Premier Eye Center, Suseong-ro 197, Suseong-Gu, Daegu 42153, Korea
| | - Su-Ho Lim
- Department of Ophthalmology, Daegu Veterans Health Service Medical Center, 60 Wolgok-Ro, Dalseo-Gu, Daegu 42835, Korea
- Correspondence: ; Tel.: +82-53-630-7572
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17
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Agrawal P, Nikhade P, Chandak M, Ikhar A, Bhonde R. Dentin Matrix Metalloproteinases: A Futuristic Approach Toward Dentin Repair and Regeneration. Cureus 2022; 14:e27946. [PMID: 36120221 PMCID: PMC9464706 DOI: 10.7759/cureus.27946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/12/2022] [Indexed: 11/05/2022] Open
Abstract
Matrix metalloproteinases (MMPs) have been linked to modulating healing during the production of tertiary dentin, as well as the liberation of physiologically active molecules and the control of developmental processes. Although efforts to protect dentin have mostly centered on preventing these proteases from doing their jobs, their role is actually much more intricate and crucial for dentin healing than anticipated. The role of MMPs as bioactive dentin matrix components involved in dentin production, repair, and regeneration is examined in the current review. The mechanical characteristics of dentin, especially those of reparative and reactionary dentin, and the established functions of MMPs in dentin production are given particular attention. Because they are essential parts of the dentin matrix, MMPs should be regarded as leading applicants for dentin regeneration.
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18
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Norville K, Skrombolas D, Ferry SL, Kearns N, Frelinger JG. A Protease Activatable Interleukin-2 Fusion Protein Engenders Antitumor Immune Responses by Interferon Gamma-Dependent and Interferon Gamma-Independent Mechanisms. J Interferon Cytokine Res 2022; 42:316-328. [PMID: 35834651 DOI: 10.1089/jir.2022.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cytokines are powerful mediators of immune responses and some, such as interleukin-2 (IL-2), have achieved dramatic responses as cancer immunotherapies. Unfortunately, systemic administration often results in deleterious side effects, prompting exploration of strategies to localize cytokine activity to the tumor microenvironment (TME). To this end, we constructed an IL-2/IL2Ra fusion protein (IL-2FP) with an MMP2/9-specific cleavage site, designed to exploit the dysregulated protease activity in the TME to selectively activate IL-2 in the tumor. To determine if TME protease activity is sufficient to cleave the FP and if FP activity is due to specific cleavage, we created Colon 38 tumor cell lines expressing similar levels of IL-2FPs with either a functional cleavage site [H11(cs-1FP)] or a scrambled, noncleavable sequence [H2(scramFP)]. H11(cs-1FP) tumors demonstrated reduced tumor growth, characterized by regressions not observed in H2(scramFP) tumors. Analysis through qRT-PCR, flow cytometry, and immunohistochemistry indicate robust CD8 responses in the H11(cs-1FP) tumors. Interferon gamma (IFNg) knockout mice revealed that the immune effects of the cleavable FP are mediated through both IFNg-dependent and IFNg-independent mechanisms. Collectively, these data suggest that matrix metalloproteinases (MMPs) in the TME can cleave the IL-2FP specifically, thus enhancing an antitumor response, and provide a rationale for further developing this approach.
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Affiliation(s)
- Karli Norville
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Denise Skrombolas
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Shannon L Ferry
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nolan Kearns
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - John G Frelinger
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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19
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Kamboj S, Harms C, Wright D, Nash A, Kumar L, Klein-Seetharaman J, Sarkar SK. Identification of allosteric fingerprints of alpha-synuclein aggregates in matrix metalloprotease-1 and substrate-specific virtual screening with single molecule insights. Sci Rep 2022; 12:5764. [PMID: 35388085 PMCID: PMC8987064 DOI: 10.1038/s41598-022-09866-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Alpha-synuclein (aSyn) has implications in pathological protein aggregations in neurodegeneration. Matrix metalloproteases (MMPs) are broad-spectrum proteases and cleave aSyn, leading to aggregation. Previous reports showed that allosteric communications between the two domains of MMP1 on collagen fibril and fibrin depend on substrates, activity, and ligands. This paper reports quantification of allostery using single molecule measurements of MMP1 dynamics on aSyn-induced aggregates by calculating Forster Resonance Energy Transfer (FRET) between two dyes attached to the catalytic and hemopexin domains of MMP1. The two domains of MMP1 prefer open conformations that are inhibited by a single point mutation E219Q of MMP1 and tetracycline, an MMP inhibitor. A two-state Poisson process describes the interdomain dynamics, where the two states and kinetic rates of interconversion between them are obtained from histograms and autocorrelations of FRET values. Since a crystal structure of aSyn-bound MMP1 is unavailable, binding poses were predicted by molecular docking of MMP1 with aSyn using ClusPro. MMP1 dynamics were simulated using predicted binding poses and compared with the experimental interdomain dynamics to identify an appropriate pose. The selected aSyn-MMP1 binding pose near aSyn residue K45 was simulated and analyzed to define conformational changes at the catalytic site. Allosteric residues in aSyn-bound MMP1 exhibiting strong correlations with the catalytic motif residues were compared with allosteric residues in free MMP1, and aSyn-specific residues were identified. The allosteric residues in aSyn-bound MMP1 are K281, T283, G292, G327, L328, E329, R337, F343, G345, N346, Y348, G353, Q354, D363, Y365, S366, S367, F368, P371, R372, V374, K375, A379, F391, A394, R399, M414, F419, V426, and C466. Shannon entropy was defined to quantify MMP1 dynamics. Virtual screening was performed against a site on selected aSyn-MMP1 binding poses, which showed that lead molecules differ between free MMP1 and substrate-bound MMP1. Also, identifying aSyn-specific allosteric residues in MMP1 enabled further selection of lead molecules. In other words, virtual screening needs to take substrates into account for potential substrate-specific control of MMP1 activity in the future. Molecular understanding of interactions between MMP1 and aSyn-induced aggregates may open up the possibility of degrading aggregates by targeting MMPs.
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Affiliation(s)
- Sumaer Kamboj
- Department of Physics, Colorado School of Mines, Golden, CO, USA
| | - Chase Harms
- Department of Physics, Colorado School of Mines, Golden, CO, USA
| | - Derek Wright
- Department of Physics, Colorado School of Mines, Golden, CO, USA
| | - Anthony Nash
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Lokender Kumar
- Department of Physics, Colorado School of Mines, Golden, CO, USA
| | | | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO, USA.
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20
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Abstract
Matrix metalloproteinases (MMPs) have been implicated not only in the regulation of developmental processes but also in the release of biologically active molecules and in the modulation of repair during tertiary dentine formation. Although efforts to preserve dentine have focused on inhibiting the activity of these proteases, their function is much more complex and necessary for dentine repair than expected. The present review explores the role of MMPs as bioactive components of the dentine matrix involved in dentine formation, repair and regeneration. Special consideration is given to the mechanical properties of dentine, including those of reactionary and reparative dentine, and the known roles of MMPs in their formation. MMPs are critical components of the dentine matrix and should be considered as important candidates in dentine regeneration.
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Affiliation(s)
- E. Guirado
- Department of Oral Biology, University of Illinois at Chicago College of Dentistry, Chicago, USA
| | - A. George
- Department of Oral Biology, University of Illinois at Chicago College of Dentistry, Chicago, USA
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21
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Harwood SL, Nielsen NS, Diep K, Jensen KT, Nielsen PK, Yamamoto K, Enghild JJ. Development of selective protease inhibitors via engineering of the bait region of human α 2-macroglobulin. J Biol Chem 2021; 297:100879. [PMID: 34139236 PMCID: PMC8267569 DOI: 10.1016/j.jbc.2021.100879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Accepted: 06/13/2021] [Indexed: 01/15/2023] Open
Abstract
Human α2-macroglobulin (A2M) is an abundant protease inhibitor in plasma, which regulates many proteolytic processes and is involved in innate immunity. A2M’s unique protease-trapping mechanism of inhibition is initiated when a protease cleaves within the exposed and highly susceptible “bait region.” As the wild-type bait region is permissive to cleavage by most human proteases, A2M is accordingly a broad-spectrum protease inhibitor. In this study, we extensively modified the bait region in order to identify any potential functionally important elements in the bait region sequence and to engineer A2M proteins with restrictive bait regions, which more selectively inhibit a target protease. A2M in which the bait region was entirely replaced by glycine-serine repeats remained fully functional and was not cleaved by any tested protease. Therefore, this bait region was designated as the “tabula rasa” bait region and used as the starting point for further bait region engineering. Cleavage of the tabula rasa bait region by specific proteases was conveyed by the insertion of appropriate substrate sequences, e.g., basic residues for trypsin. Screening and optimization of tabula rasa bait regions incorporating matrix metalloprotease 2 (MMP2) substrate sequences produced an A2M that was specifically cleaved by MMPs and inhibited MMP2 cleavage activity as efficiently as wild-type A2M. We propose that this approach can be used to develop A2M-based protease inhibitors, which selectively inhibit target proteases, which might be applied toward the clinical inhibition of dysregulated proteolysis as occurs in arthritis and many types of cancer.
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Affiliation(s)
- Seandean Lykke Harwood
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Khang Diep
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Kazuhiro Yamamoto
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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22
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Conformation-Specific Inhibitory Anti-MMP-7 Monoclonal Antibody Sensitizes Pancreatic Ductal Adenocarcinoma Cells to Chemotherapeutic Cell Kill. Cancers (Basel) 2021; 13:cancers13071679. [PMID: 33918254 PMCID: PMC8038143 DOI: 10.3390/cancers13071679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Matrix metalloproteases (MMPs) undergo post-translational modifications including pro-domain shedding. The activated forms of these enzymes are effective drug targets, but generating potent biological inhibitors against them remains challenging. We report the generation of anti-MMP-7 inhibitory monoclonal antibody (GSM-192), using an alternating immunization strategy with an active site mimicry antigen and the activated enzyme. Our protocol yielded highly selective anti-MMP-7 monoclonal antibody, which specifically inhibits MMP-7's enzyme activity with high affinity (IC50 = 132 ± 10 nM). The atomic model of the MMP-7-GSM-192 Fab complex exhibited antibody binding to unique epitopes at the rim of the enzyme active site, sterically preventing entry of substrates into the catalytic cleft. In human PDAC biopsies, tissue staining with GSM-192 showed characteristic spatial distribution of activated MMP-7. Treatment with GSM-192 in vitro induced apoptosis via stabilization of cell surface Fas ligand and retarded cell migration. Co-treatment with GSM-192 and chemotherapeutics, gemcitabine and oxaliplatin elicited a synergistic effect. Our data illustrate the advantage of precisely targeting catalytic MMP-7 mediated disease specific activity.
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23
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Ozols M, Eckersley A, Platt CI, Stewart-McGuinness C, Hibbert SA, Revote J, Li F, Griffiths CEM, Watson REB, Song J, Bell M, Sherratt MJ. Predicting Proteolysis in Complex Proteomes Using Deep Learning. Int J Mol Sci 2021; 22:3071. [PMID: 33803033 PMCID: PMC8002881 DOI: 10.3390/ijms22063071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/27/2022] Open
Abstract
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins to photo-oxidation. However, predicting protein susceptibility to endogenous proteases remains challenging. Here, we aim to develop bioinformatics tools to (i) predict cleavage site locations (and hence putative protein susceptibilities) and (ii) compare the predicted vulnerabilities of skin proteins to protease- and ROS-mediated proteolysis. The first goal of this study was to experimentally evaluate the ability of existing protease cleavage site prediction models (PROSPER and DeepCleave) to identify experimentally determined MMP9 cleavage sites in two purified proteins and in a complex human dermal fibroblast-derived extracellular matrix (ECM) proteome. We subsequently developed deep bidirectional recurrent neural network (BRNN) models to predict cleavage sites for 14 tissue proteases. The predictions of the new models were tested against experimental datasets and combined with amino acid composition analysis (to predict ultraviolet radiation (UVR)/ROS susceptibility) in a new web app: the Manchester proteome susceptibility calculator (MPSC). The BRNN models performed better in predicting cleavage sites in native dermal ECM proteins than existing models (DeepCleave and PROSPER), and application of MPSC to the skin proteome suggests that: compared with the elastic fiber network, fibrillar collagens may be susceptible primarily to protease-mediated proteolysis. We also identify additional putative targets of oxidative damage (dermatopontin, fibulins and defensins) and protease action (laminins and nidogen). MPSC has the potential to identify potential targets of proteolysis in disparate tissues and disease states.
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Affiliation(s)
- Matiss Ozols
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (A.E.); (C.I.P.); (C.S.-M.); (S.A.H.)
| | - Alexander Eckersley
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (A.E.); (C.I.P.); (C.S.-M.); (S.A.H.)
| | - Christopher I. Platt
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (A.E.); (C.I.P.); (C.S.-M.); (S.A.H.)
| | - Callum Stewart-McGuinness
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (A.E.); (C.I.P.); (C.S.-M.); (S.A.H.)
| | - Sarah A. Hibbert
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (A.E.); (C.I.P.); (C.S.-M.); (S.A.H.)
| | - Jerico Revote
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia;
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia;
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3800, Australia;
| | - Christopher E. M. Griffiths
- Centre for Dermatology Research, Faculty of Biology, Medicine and Health, and Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (C.E.M.G.); (R.E.B.W.)
- NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Rachel E. B. Watson
- Centre for Dermatology Research, Faculty of Biology, Medicine and Health, and Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (C.E.M.G.); (R.E.B.W.)
- NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Jiangning Song
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia;
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Mike Bell
- Research and Development, Walgreens Boots Alliance, Thane Road, Nottingham NG90 1BS, UK;
| | - Michael J. Sherratt
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (A.E.); (C.I.P.); (C.S.-M.); (S.A.H.)
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Jiang T, Liu C, Xu X, He B, Mo R. Formation Mechanism and Biomedical Applications of Protease-Manipulated Peptide Assemblies. Front Bioeng Biotechnol 2021; 9:598050. [PMID: 33718335 PMCID: PMC7952644 DOI: 10.3389/fbioe.2021.598050] [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: 08/23/2020] [Accepted: 02/04/2021] [Indexed: 12/02/2022] Open
Abstract
Exploiting enzyme-catalyzed reactions to manipulate molecular assembly has been considered as an attractive bottom-up nanofabrication approach to developing a variety of nano-, micro-, and macroscale structures. Upon enzymatic catalysis, peptides and their derivatives transform to assemblable building blocks that form ordered architecture by non-covalent interactions. The peptide assemblies with unique characteristics have great potential for applications in bionanotechnology and biomedicine. In this mini review, we describe typical mechanisms of the protease-instructed peptide assembly via bond-cleaving or bond-forming reactions, and outline biomedical applications of the peptide assemblies, such as drug depot, sustained release, controlled release, gelation-regulated cytotoxicity, and matrix construction.
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Affiliation(s)
- Tianyue Jiang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Chendan Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Xiao Xu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Ran Mo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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25
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Quantitative profiling of protease specificity. PLoS Comput Biol 2021; 17:e1008101. [PMID: 33617527 PMCID: PMC7932537 DOI: 10.1371/journal.pcbi.1008101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/04/2021] [Accepted: 01/28/2021] [Indexed: 12/30/2022] Open
Abstract
Proteases are an important class of enzymes, whose activity is central to many physiologic and pathologic processes. Detailed knowledge of protease specificity is key to understanding their function. Although many methods have been developed to profile specificities of proteases, few have the diversity and quantitative grasp necessary to fully define specificity of a protease, both in terms of substrate numbers and their catalytic efficiencies. We have developed a concept of “selectome”; the set of substrate amino acid sequences that uniquely represent the specificity of a protease. We applied it to two closely related members of the Matrixin family–MMP-2 and MMP-9 by using substrate phage display coupled with Next Generation Sequencing and information theory-based data analysis. We have also derived a quantitative measure of substrate specificity, which accounts for both the number of substrates and their relative catalytic efficiencies. Using these advances greatly facilitates elucidation of substrate selectivity between closely related members of a protease family. The study also provides insight into the degree to which the catalytic cleft defines substrate recognition, thus providing basis for overcoming two of the major challenges in the field of proteolysis: 1) development of highly selective activity probes for studying proteases with overlapping specificities, and 2) distinguishing targeted proteolysis from bystander proteolytic events. Proteases and proteolysis are intimately involved in virtually all biological processes from embryonic development to programmed cell death and cellular protein recycling. As the only irreversible posttranslational modification, proteolysis represents a committed step in regulation of biological networks and pathways. Imbalance of proteolytic activity has catastrophic implications and is the basis of many genetic disorders as well as a multitude of pathological states of varying etiologies. To understand protease function, one must gain insight into the repertoires of substrates targeted by these enzymes. As many proteases recognize a wide variety of sequences in proteins, it is a challenge to establish if a particular cleavage represents a targeted or a bystander proteolytic event. In addition, since many proteases have overlapping specificities, especially among closely related members of the same gene families, it is a challenge to develop highly selective tools for studying or inhibition of these enzymes. In this work, we used two closely related proteases (MMP-2 and 9) as a model system for development of an information theory-based approach to quantification of substrate specificity and demonstrated its potential for distinguishing between the target and bystander proteolytic events as well as for uncovering selectivity between closely related proteases.
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De-shielding of activatable cell-penetrating peptides: recognizing and releasing in activation process. RESEARCH ON CHEMICAL INTERMEDIATES 2021. [DOI: 10.1007/s11164-020-04339-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wang S, Tian X, Liu D, Zhang X, Yan C, Han Y. TRPV5 attenuates abdominal aortic aneurysm in mice by regulating KLF4-dependent phenotype switch of aortic vascular smooth muscle cells. Arch Biochem Biophys 2020; 698:108724. [PMID: 33309615 DOI: 10.1016/j.abb.2020.108724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Abdominal aortic aneurysm (AAA) is a fatal vascular disease with insidious symptoms. However, the mechanism behind its development remains unclear. The transient receptor potential vanilloid (TRPV) family has crucial protective effects against cardiovascular diseases, but the role of TRPV5 in AAA has yet to be reported. In this study, ApoE-/- mice were intraperitoneally injected with AAV-GFP or AAV-TRPV5. After 30 days, mice were further administered with angiotensin II (Ang II, 1.44 mg/kg/day) by using osmotic pumps to induce the AAA model or Saline for 28 days, (i.e., Saline + AAV-GFP, Saline + AAV-TRPV5, Ang II + AAV-GFP and Ang II + AAV-TRPV5 groups were established). Compared with the control group, the incidence of AAA and the maximal diameter of the abdominal aorta markedly decreased in Ang II + AAV-TRPV5, which was detected by vascular ultrasound at 28 day. Meanwhile, less collagen and elastin degradation were observed in the Ang II + AAV-TRPV5 group by using Masson and Elastin stains. Moreover, more α-SMA and less MMP2 was observed in the abdominal aortas collected at 28 day by immunohistochemistry. In vitro, primary mouse vascular smooth muscle cells (VSMCs) were treated with Ang II (1 μM) to induce phenotype switch. Sh-TRPV5 and AdTRPV5 were used to transfect VSMCs. PCR and Western blotting were used to access the expression of contractile marker, including α-SMA and SM-22α. The results showed that the mRNA and protein level of α-SMA and SM-22α were decreased under the stimulation of Ang II, but could be attenuated by TRPV5 overexpression. The cell scratch assay demonstrated that the migration ability of VSMCs was increased in Ang II treated group and could be ameliorated by TRPV5 overexpression. Above all, VSMCs transformed from the contractile into secretory phenotype under Ang II stimuli, but could be rescued by TRPV5 overexpression. Furthermore, TRPV5 overexpression suppressed the increased expression of KLF4 induced by Ang II treatment in VSMCs. The data demonstrated that TRPV5 could inhibit AAA formation and play a critical role in the VSMC phenotype switch by downregulating KLF4, suggesting TRPV5 as a new strategy for treating AAA.
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Affiliation(s)
- Shuo Wang
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, China; Department of Cardiology and Cardiovascular Research Institute, General Hospital of Northern Theater Command, Shenyang, China
| | - Xiaoxiang Tian
- Department of Cardiology and Cardiovascular Research Institute, General Hospital of Northern Theater Command, Shenyang, China
| | - Dan Liu
- Department of Cardiology and Cardiovascular Research Institute, General Hospital of Northern Theater Command, Shenyang, China
| | - Xiaolin Zhang
- Department of Cardiology and Cardiovascular Research Institute, General Hospital of Northern Theater Command, Shenyang, China
| | - Chenghui Yan
- Department of Cardiology and Cardiovascular Research Institute, General Hospital of Northern Theater Command, Shenyang, China
| | - Yaling Han
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, China; Department of Cardiology and Cardiovascular Research Institute, General Hospital of Northern Theater Command, Shenyang, China.
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Kumar L, Planas-Iglesias J, Harms C, Kamboj S, Wright D, Klein-Seetharaman J, Sarkar SK. Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin. Sci Rep 2020; 10:20615. [PMID: 33244162 PMCID: PMC7692495 DOI: 10.1038/s41598-020-77699-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 11/13/2020] [Indexed: 01/18/2023] Open
Abstract
The roles of protein conformational dynamics and allostery in function are well-known. However, the roles that interdomain dynamics have in function are not entirely understood. We used matrix metalloprotease-1 (MMP1) as a model system to study the relationship between interdomain dynamics and activity because MMP1 has diverse substrates. Here we focus on fibrin, the primary component of a blood clot. Water-soluble fibrinogen, following cleavage by thrombin, self-polymerize to form water-insoluble fibrin. We studied the interdomain dynamics of MMP1 on fibrin without crosslinks using single-molecule Forster Resonance Energy Transfer (smFRET). We observed that the distance between the catalytic and hemopexin domains of MMP1 increases or decreases as the MMP1 activity increases or decreases, respectively. We modulated the activity using (1) an active site mutant (E219Q) of MMP1, (2) MMP9, another member of the MMP family that increases the activity of MMP1, and (3) tetracycline, an inhibitor of MMP1. We fitted the histograms of smFRET values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We modeled the dynamics as a two-state Poisson process and calculated the kinetic rates from the histograms and autocorrelations. Activity-dependent interdomain dynamics may enable allosteric control of the MMP1 function.
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Affiliation(s)
- Lokender Kumar
- Department of Physics, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401, USA
| | - Joan Planas-Iglesias
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
| | - Chase Harms
- Department of Physics, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401, USA
| | - Sumaer Kamboj
- Department of Physics, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401, USA
| | - Derek Wright
- Department of Physics, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401, USA
| | - Judith Klein-Seetharaman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Department of Chemistry, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401, USA
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401, USA.
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Matrix Metalloproteinase 14 Mediates APP Proteolysis and Lysosomal Alterations Induced by Oxidative Stress in Human Neuronal Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:5917187. [PMID: 33282112 PMCID: PMC7685830 DOI: 10.1155/2020/5917187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022]
Abstract
The alteration of amyloid precursor protein (APP) proteolysis is a hallmark of Alzheimer's disease (AD). Recent studies have described noncanonical pathways of APP processing that seem partly executed by lysosomal enzymes. Our laboratory's in vitro human SK-N-MC model has shown that oxidative stress (OS) alters the lysosomal degradation pathway and the processing/metabolism of APP. The present study identifies the lysosomal protein matrix metalloproteinase 14 (MMP14) as a protease involved in the APP noncanonical processing. Previous expression analyses of the above cells showed MMP14 to be overexpressed under OS. In the present work, its role in changes in OS-induced APP proteolysis and lysosomal load was examined. The results show that MMP14 mediates the accumulation of an ≈85 kDa N-terminal APP fragment and increases the lysosome load induced by OS. These results were validated in neurons and neural progenitor cells generated from the induced pluripotent stem cells of patients with sporadic AD, reinforcing the idea that MMP14 may offer a therapeutic target in this disease.
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Kumar L, Nash A, Harms C, Planas-Iglesias J, Wright D, Klein-Seetharaman J, Sarkar SK. Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1. Biophys J 2020; 119:360-374. [PMID: 32585130 PMCID: PMC7376139 DOI: 10.1016/j.bpj.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 11/23/2022] Open
Abstract
An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intradomain dynamics occurring at picosecond to millisecond timescales. However, the correlation between interdomain dynamics and the function of a protein is poorly understood. Here, we show that communications between the catalytic and hemopexin domains of matrix metalloprotease-1 (MMP1) on type 1 collagen fibrils correlate with its activity. Using single-molecule Förster resonance energy transfer, we identified functionally relevant open conformations in which the two MMP1 domains are well separated, which were significantly absent for catalytically inactive point mutant (E219Q) of MMP1 and could be modulated by an inhibitor or an enhancer of activity. The observed relevance of open conformations resolves the debate about the roles of open and closed MMP1 structures in function. We fitted the histograms of single-molecule Förster resonance energy transfer values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We used a two-state Poisson process to describe the dynamics and calculate the kinetic rates from the fit parameters. All-atom and coarse-grained simulations reproduced some of the experimental features and revealed substrate-dependent MMP1 dynamics. Our results suggest that an interdomain separation facilitates opening up the catalytic pocket so that the collagen chains come closer to the MMP1 active site. Coordination of functional conformations at different parts of MMP1 occurs via allosteric communications that can take place via interactions mediated by collagen even if the linker between the domains is absent. Modeling dynamics as a Poisson process enables connecting the picosecond timescales of molecular dynamics simulations with the millisecond timescales of single-molecule measurements. Water-soluble MMP1 interacting with water-insoluble collagen fibrils poses challenges for biochemical studies that the single-molecule tracking can overcome for other insoluble substrates. Interdomain communications are likely important for multidomain proteins.
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Affiliation(s)
- Lokender Kumar
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Anthony Nash
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Chase Harms
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Joan Planas-Iglesias
- Warwick Medical School, University of Warwick, Coventry, United Kingdom; Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Derek Wright
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Judith Klein-Seetharaman
- Warwick Medical School, University of Warwick, Coventry, United Kingdom; Department of Chemistry, Colorado School of Mines, Golden, Colorado
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, Colorado.
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31
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Poreba M. Protease-activated prodrugs: strategies, challenges, and future directions. FEBS J 2020; 287:1936-1969. [PMID: 31991521 DOI: 10.1111/febs.15227] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023]
Abstract
Proteases play critical roles in virtually all biological processes, including proliferation, cell death and survival, protein turnover, and migration. However, when dysregulated, these enzymes contribute to the progression of multiple diseases, with cancer, neurodegenerative disorders, inflammation, and blood disorders being the most prominent examples. For a long time, disease-associated proteases have been used for the activation of various prodrugs due to their well-characterized catalytic activity and ability to selectively cleave only those substrates that strictly correspond with their active site architecture. To date, versatile peptide sequences that are cleaved by proteases in a site-specific manner have been utilized as bioactive linkers for the targeted delivery of multiple types of cargo, including fluorescent dyes, photosensitizers, cytotoxic drugs, antibiotics, and pro-antibodies. This platform is highly adaptive, as multiple protease-labile conjugates have already been developed, some of which are currently in clinical use for cancer treatment. In this review, recent advancements in the development of novel protease-cleavable linkers for selective drug delivery are described. Moreover, the current limitations regarding the selectivity of linkers are discussed, and the future perspectives that rely on the application of unnatural amino acids for the development of highly selective peptide linkers are also presented.
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Affiliation(s)
- Marcin Poreba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Poland
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32
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Ji X, Xie S, Jiao Y, Zhang X, Sun D, Yang VC, Wang M, He H, Sun L. MT1-MMP activatable fluorogenic probes with enhanced specificity via high-affinity peptide conjugation for tumor imaging. Biomater Sci 2020; 8:2308-2317. [PMID: 32186291 DOI: 10.1039/c9bm02007a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Overlapping substrate specificities within the family of matrix metalloproteinases (MMPs), usually caused by their highly conserved structural topology, increase the potential for a substrate to be cleaved by multiple enzymes within this family, which leads to the decrease in the selectivity of MMP substrate-based probes. To resolve this issue, MT1-MMP activatable fluorogenic probes for tumor detection with enhanced specificity were developed by combining a fluorescence resonance energy transfer (FRET) peptide substrate and its specific binding peptide with different lengths of linkers. The specificity of the probes increased profiting from the high affinity of the MT1-MMP specific binding peptide while keeping the ability to amplify the output imaging signals in response to MMP activity with the FRET substrate. Enzyme kinetics analysis clearly demonstrated that the conjugation of P-1 and MT1-AF7p enhanced both the specificity and selectivity of the fluorogenic probes for MT1-MMP, and introducing a linker composed of 12 PEG subunits into these two fragments led to optimized specificity and selectivity of the fluorogenic probe for MT1-MMP. Both in vitro and in vivo results revealed that the imaging probe with the linker composed of 12 PEG subunits based on our designed strategy could be effectively applied for MT1-MMP positive tumor imaging. Since this strategy for enhancing the specificity of protease sensing probes can be applied to other proteases and is not just limited to MT1-MMP, it is an appealing platform to achieve selective tumor imaging.
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Affiliation(s)
- Xiuru Ji
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
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Matrix Metalloproteinase Triple-Helical Peptide Inhibitors: Potential Cross-Reactivity with Caspase-11. Molecules 2019; 24:molecules24234355. [PMID: 31795279 PMCID: PMC6930605 DOI: 10.3390/molecules24234355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/15/2022] Open
Abstract
Triple-helical peptide inhibitors (THPIs) of matrix metalloproteinases (MMPs) have recently been demonstrated to be effective in a variety of animal models of disease, coincidental with knockout studies. However, passenger mutations have been described in MMP knockout mice that impact the activity of other proteins, including caspase-11. Thus, it is possible that the results observed with THPIs may be based on inhibition of caspase-11, not MMPs. The present study evaluated whether THPIs were cross-reactive with caspase-11. Two different THPIs were tested, one that is known to inhibit MMP-1 and MMP-8 (GlyΨ{PO2H-CH2}Ile-His-Lys-Gln THPI) and one that is selective for MMP-2 and MMP-9 (α1(V)GlyΨ{PO2H-CH2}Val [mep14,32,Flp15,33] THPI). No inhibition of caspase-11 was observed with GlyΨ{PO2H–CH2}Ile–His–Lys–Gln THPI, even at an inhibitor concentration of 5 μM, while 5 μM α1(V)GlyΨ{PO2H-CH2}Val [mep14,32,Flp15,33] THPI exhibited 40% inhibition of caspase-11. Further testing of GlyΨ{PO2H-CH2}Ile-His-Lys-Gln THPI revealed nM inhibition of MMP-2, MMP-9, and MMP-13. Thus, the effectiveness of GlyΨ{PO2H-CH2}Ile-His-Lys-Gln THPI observed in a sepsis animal model may not be due to caspase-11 inhibition, but may be due to broader MMP inhibition than previously thought.
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34
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Fedonin GG, Eroshkin A, Cieplak P, Matveev EV, Ponomarev GV, Gelfand MS, Ratnikov BI, Kazanov MD. Predictive models of protease specificity based on quantitative protease-activity profiling data. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140253. [PMID: 31330204 DOI: 10.1016/j.bbapap.2019.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/09/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
Bioinformatics-based prediction of protease substrates can help to elucidate regulatory proteolytic pathways that control a broad range of biological processes such as apoptosis and blood coagulation. The majority of published predictive models are position weight matrices (PWM) reflecting specificity of proteases toward target sequence. These models are typically derived from experimental data on positions of hydrolyzed peptide bonds and show a reasonable predictive power. New emerging techniques that not only register the cleavage position but also measure catalytic efficiency of proteolysis are expected to improve the quality of predictions or at least substantially reduce the number of tested substrates required for confident predictions. The main goal of this study was to develop new prediction models based on such data and to estimate the performance of the constructed models. We used data on catalytic efficiency of proteolysis measured for eight major human matrix metalloproteinases to construct predictive models of protease specificity using a variety of regression analysis techniques. The obtained results suggest that efficiency-based (quantitative) models show a comparable performance with conventional PWM-based algorithms, while less training data are required. The derived list of candidate cleavage sites in human secreted proteins may serve as a starting point for experimental analysis.
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Affiliation(s)
- Gennady G Fedonin
- Central Research Institute of Epidemiology, Moscow 111123, Russia; A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Alexey Eroshkin
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Piotr Cieplak
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Gennady V Ponomarev
- A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Moscow 121205, Russia; National Research University Higher School of Economics, Moscow 101000, Russia
| | - Boris I Ratnikov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Marat D Kazanov
- A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117997, Russia.
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Nair RP, Timiri Shanmugam PS, Sunavala-Dossabhoy G. Discretionary Transduction of MMP-Sensitized Tousled in Head and Neck Cancer. MOLECULAR THERAPY-ONCOLYTICS 2019; 14:57-65. [PMID: 31011632 PMCID: PMC6463741 DOI: 10.1016/j.omto.2019.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/15/2019] [Indexed: 12/27/2022]
Abstract
Oral radiotoxicity is often a limiting factor in cancer treatment. Previously, we demonstrated that transfer of cell-permeable, TAT-fusion Tousled-like kinase 1B (TLK1B) protein in salivary glands effectively mitigates radiation-induced salivary dysfunction. However, similar to most radioprotectors, TLK1B can carry the risk of limiting cancer treatment efficacy. The central goal of the study was, therefore, to reengineer TLK1B as a selective radioprotector of normal cells. Degradation of the extracellular matrix by proteases such as matrix metalloproteinases (MMPs) is a hallmark of aggressive tumors. Increased expression of membrane type 1-MMP (MT1-MMP; also called MMP14) is observed in a variety of cancers including head and neck squamous cell carcinoma (HNSCC). To limit TLK1B transduction to normal cells, we rendered the protein susceptible to MT1-MMP cleavage on the premise that high expression of MT1-MMP on the cell surface of HNSCC will suppress TLK1B internalization. Two optimal MT1-MMP-sensitive sequences (MS) were identified that when incorporated in TAT-TLK1B excluded its cellular entry in HNSCC, SCC40, but not immortalized salivary acinar cells, NS-SV-AC. Importantly, administration of MS-harboring TAT-TLK1B did not affect the sensitivity of tumors to radiation in a nude mouse xenograft tumor model. We conclude that a MMP-sensitive TLK1B can be an attractive therapeutic to allay salivary radiotoxicity without compromising cancer treatment efficacy.
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Affiliation(s)
- Renjith Parameswaran Nair
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA
| | - Prakash Srinivasan Timiri Shanmugam
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA
| | - Gulshan Sunavala-Dossabhoy
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA
- Feist-Weiller Cancer Center, Shreveport, LA, USA
- Corresponding author: Gulshan Sunavala-Dossabhoy, Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA.
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Shim G, Le QV, Suh J, Choi S, Kim G, Choi HG, Kim YB, Macgregor RB, Oh YK. Sequential activation of anticancer therapy triggered by tumor microenvironment-selective imaging. J Control Release 2019; 298:110-119. [DOI: 10.1016/j.jconrel.2019.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 01/03/2019] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
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37
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Matrix metalloprotease triggered bioresponsive drug delivery systems – Design, synthesis and application. Eur J Pharm Biopharm 2018; 131:189-202. [DOI: 10.1016/j.ejpb.2018.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 08/22/2018] [Indexed: 01/06/2023]
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Sun L, Xie S, Ji X, Zhang J, Wang D, Lee SJ, Lee H, He H, Yang VC. MMP-2-responsive fluorescent nanoprobes for enhanced selectivity of tumor cell uptake and imaging. Biomater Sci 2018; 6:2619-2626. [PMID: 30109310 DOI: 10.1039/c8bm00593a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is difficult to develop highly selective substrate-based fluorescent nanoprobes for specific matrix metalloproteinases (MMPs) due to overlapping substrate specificities among the family of MMP enzymes. To resolve this issue, we have developed novel fluorescent nanoprobes that are highly selective for soluble MMP-2. Herein, MMP-2-responsive nanoprobes were prepared by immobilizing fluorescent fusion proteins on nickel ferrite nanoparticles via the His-tag nickel chelation mechanism. The fusion protein consisted of a fluorescent mCherry protein with a cell penetrating peptide (CPP) moiety. An MMP-2 cleavage site was also introduced within the fusion protein, which was directly linked to the nickel ferrite nanoparticles. The selectivity of nanoprobes was modulated by hiding the cleavage site of MMP-2 substrates deeply inside the system, which could result in strong steric hindrance between the nanoprobes and MMPs, especially for membrane-tethered MMPs such as MMP-14. A cell-based assay demonstrated that the nanoprobes could only be activated by tumor cells secreting soluble MMP-2, but not membrane-tethered MMP-14. To further evaluate the contribution of the steric hindrance effect on the nanoprobes, a truncated recombinant MMP-14 was employed to confer their cleavage activity as compared to native membrane-tethered MMP-14. Furthermore, a designed probe with a diminished steric hindrance effect was proved to be activated by membrane-tethered type MMP-14. The results indicated that the design of fluorescent nanoprobes employing the steric hindrance effect can greatly enhance the selectivity of MMP-responsive nanoprobes realizing the specific detection of soluble MMP-2 in a tumor microenvironment. We believe that highly selective MMP-2-responsive fluorescent nanoprobes have broad impacts on biomedical applications including molecular imaging and labeling for tumor detection.
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Affiliation(s)
- Lu Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
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Tokmina-Roszyk M, Fields GB. Dissecting MMP P 10' and P 11' subsite sequence preferences, utilizing a positional scanning, combinatorial triple-helical peptide library. J Biol Chem 2018; 293:16661-16676. [PMID: 30185620 DOI: 10.1074/jbc.ra118.003266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/01/2018] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that remodel the extracellular matrix environment and mitigate outside-in signaling. Loss of regulation of MMP activity plays a role in numerous pathological states. In particular, aberrant collagenolysis affects tumor invasion and metastasis, osteoarthritis, and cardiovascular and neurodegenerative diseases. To evaluate the collagen sequence preferences of MMPs, a positional scanning synthetic combinatorial library was synthesized herein and was used to investigate the P10' and P11' substrate subsites. The scaffold for the library was a triple-helical peptide mimic of the MMP cleavage site in types I-III collagen. A FRET-based enzyme activity assay was used to evaluate the sequence preferences of eight MMPs. Deconvolution of the library data revealed distinct motifs for several MMPs and discrimination among closely related MMPs. On the basis of the screening results, several individual peptides were designed and evaluated. A triple-helical substrate incorporating Asp-Lys in the P10'-P11' subsites offered selectivity between MMP-14 and MMP-15, whereas Asp-Lys or Trp-Lys in these subsites discriminated between MMP-2 and MMP-9. Future screening of additional subsite positions will enable the design of selective triple-helical MMP probes that could be used for monitoring in vivo enzyme activity and enzyme-facilitated drug delivery. Furthermore, selective substrates could serve as the basis for the design of specific triple-helical peptide inhibitors targeting only those MMPs that play a detrimental role in a disease of interest.
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Affiliation(s)
- Michal Tokmina-Roszyk
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and
| | - Gregg B Fields
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and .,the Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458
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Arkadash V, Radisky ES, Papo N. Combinatorial engineering of N-TIMP2 variants that selectively inhibit MMP9 and MMP14 function in the cell. Oncotarget 2018; 9:32036-32053. [PMID: 30174795 PMCID: PMC6112833 DOI: 10.18632/oncotarget.25885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/21/2018] [Indexed: 12/21/2022] Open
Abstract
Developing selective inhibitors for proteolytic enzymes that share high sequence homology and structural similarity is important for achieving high target affinity and functional specificity. Here, we used a combination of yeast surface display and dual-color selective library screening to obtain selective inhibitors for each of the matrix metalloproteinases (MMPs) MMP14 and MMP9 by modifying the non-specific N-terminal domain of the tissue inhibitor of metalloproteinase-2 (N-TIMP2). We generated inhibitor variants with 30- to 1175-fold improved specificity to each of the proteases, respectively, relative to wild type N-TIMP2. These biochemical results accurately predicted the selectivity and specificity obtained in cell-based assays. In U87MG cells, the activation of MMP2 by MMP14 was inhibited by MMP14-selective blockers but not MMP9-specific inhibitors. Target specificity was also demonstrated in MCF-7 cells stably expressing either MMP14 or MMP9, with only the MMP14-specific inhibitors preventing the mobility of MMP14-expressing cells. Similarly, the mobility of MMP9-expressing cells was inhibited by the MMP9-specific inhibitors, yet was not altered by the MMP14-specific inhibitors. The strategy developed in this study for improving the specificity of an otherwise broad-spectrum inhibitor will likely enhance our understanding of the basis for target specificity of inhibitors to proteolytic enzymes, in general, and to MMPs, in particular. We, moreover, envision that this study could serve as a platform for the development of next-generation, target-specific therapeutic agents. Finally, our methodology can be extended to other classes of proteolytic enzymes and other important target proteins.
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Affiliation(s)
- Valeria Arkadash
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Affiliation(s)
- Jacquelyn S. Fetrow
- Office of the President, Albright College, Reading, Pennsylvania, United States of America
- * E-mail:
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
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Gioia M, Fasciglione GF, Sbardella D, Sciandra F, Casella M, Camerini S, Crescenzi M, Gori A, Tarantino U, Cozza P, Brancaccio A, Coletta M, Bozzi M. The enzymatic processing of α-dystroglycan by MMP-2 is controlled by two anchoring sites distinct from the active site. PLoS One 2018; 13:e0192651. [PMID: 29447293 PMCID: PMC5813964 DOI: 10.1371/journal.pone.0192651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/26/2018] [Indexed: 11/19/2022] Open
Abstract
Dystroglycan (DG) is a membrane receptor, belonging to the dystrophin-glycoprotein complex (DGC) and formed by two subunits, α-dystroglycan (α-DG) and β-dystroglycan (β -DG). The C-terminal domain of α-DG and the N-terminal extracellular domain of β -DG are connected, providing a link between the extracellular matrix and the cytosol. Under pathological conditions, such as cancer and muscular dystrophies, DG may be the target of metalloproteinases MMP-2 and MMP-9, contributing to disease progression. Previously, we reported that the C-terminal domain α-DG (483–628) domain is particularly susceptible to the catalytic activity of MMP-2; here we show that the α-DG 621–628 region is required to carry out its complete digestion, suggesting that this portion may represent a MMP-2 anchoring site. Following this observation, we synthesized an α-DG based-peptide, spanning the (613–651) C-terminal region. The analysis of the kinetic and thermodynamic parameters of the whole and the isolated catalytic domain of MMP-2 (cdMMP-2) has shown its inhibitory properties, indicating the presence of (at least) two binding sites for the peptide, both located within the catalytic domain, only one of the two being topologically distinct from the catalytic active groove. However, the different behavior between whole MMP-2 and cdMMP-2 envisages the occurrence of an additional binding site for the peptide on the hemopexin-like domain of MMP-2. Interestingly, mass spectrometry analysis has shown that α-DG (613–651) peptide is cleavable even though it is a very poor substrate of MMP-2, a feature that renders this molecule a promising template for developing a selective MMP-2 inhibitor.
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Affiliation(s)
- Magda Gioia
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
- * E-mail: (MG); (MB)
| | - Giovanni Francesco Fasciglione
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
| | - Diego Sbardella
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
| | | | | | | | | | | | - Umberto Tarantino
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Paola Cozza
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Andrea Brancaccio
- CNR Institute for Molecular Recognition, Roma Italy
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
| | - Manuela Bozzi
- CNR Institute for Molecular Recognition, Roma Italy
- Institute of Biochemistry and Clinical Biochemistry, Catholic University, Roma Italy
- * E-mail: (MG); (MB)
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Kretz CA, Tomberg K, Van Esbroeck A, Yee A, Ginsburg D. High throughput protease profiling comprehensively defines active site specificity for thrombin and ADAMTS13. Sci Rep 2018; 8:2788. [PMID: 29434246 PMCID: PMC5809430 DOI: 10.1038/s41598-018-21021-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/29/2018] [Indexed: 12/20/2022] Open
Abstract
We have combined random 6 amino acid substrate phage display with high throughput sequencing to comprehensively define the active site specificity of the serine protease thrombin and the metalloprotease ADAMTS13. The substrate motif for thrombin was determined by >6,700 cleaved peptides, and was highly concordant with previous studies. In contrast, ADAMTS13 cleaved only 96 peptides (out of >107 sequences), with no apparent consensus motif. However, when the hexapeptide library was substituted into the P3-P3′ interval of VWF73, an exosite-engaging substrate of ADAMTS13, 1670 unique peptides were cleaved. ADAMTS13 exhibited a general preference for aliphatic amino acids throughout the P3-P3′ interval, except at P2 where Arg was tolerated. The cleaved peptides assembled into a motif dominated by P3 Leu, and bulky aliphatic residues at P1 and P1′. Overall, the P3-P2′ amino acid sequence of von Willebrand Factor appears optimally evolved for ADAMTS13 recognition. These data confirm the critical role of exosite engagement for substrates to gain access to the active site of ADAMTS13, and define the substrate recognition motif for ADAMTS13. Combining substrate phage display with high throughput sequencing is a powerful approach for comprehensively defining the active site specificity of proteases.
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Affiliation(s)
- Colin A Kretz
- Department of Medicine, McMaster University and the Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.
| | - Kärt Tomberg
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Van Esbroeck
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Yee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute and Departments of Internal Medicine and Pediatrics, University of Michigan, Ann Arbor, MI, USA
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44
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Sun L, Xie S, Qi J, Liu E, Liu D, Liu Q, Chen S, He H, Yang VC. Cell-Permeable, MMP-2 Activatable, Nickel Ferrite and His-Tagged Fusion Protein Self-Assembled Fluorescent Nanoprobe for Tumor Magnetic-Targeting and Imaging. ACS APPLIED MATERIALS & INTERFACES 2017; 9:39209-39222. [PMID: 29058417 DOI: 10.1021/acsami.7b12918] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Matrix metalloproteinases (MMPs) activatable imaging probe has been explored for tumor detection. However, activation of the probe is mainly done in the extracellular space without intracellular uptake of the probe for more sensitivity. Although cell-penetrating peptides (CPPs) have been demonstrated to enable intracellular delivery of the imaging probe, they nevertheless encounter off-target delivery of the cargos to normal tissues. Herein, we have developed a dual MMP-2-activatable and tumor cell-permeable magnetic nanoprobe to simultaneously achieve selective and intracellular tumor imaging. This novel imaging probe was constructed by self-assembling a hexahistidine-tagged (His-tagged) fluorescent fusion protein chimera and nickel ferrite nanoparticles via a chelation mechanism. The His-tagged fluorescent protein chimera consisted of a red fluorescent protein mCherry that acted as the fluorophore, the low-molecular-weight protamine peptide as the CPP, and the MMP-2 cleavage sequence fused with the hexahistidine tag, whereas the nickel ferrite nanoparticles functioned as the His-tagged protein binder and also the fluorescent quencher. Both in vitro and in vivo results revealed that this imaging probe would not only remain nonpermeable to normal tissues, thereby offsetting the nonselective cellular uptake, but was also suppressed of fluorescent signals during magnetic tumor-targeting in the circulation, primarily because of the masking of the CPP activity and quenching of the fluorophore by the associated NiFe2O4 nanoparticles. However, these properties were recovered or "turned on" by the action of tumor-associated MMP-2 stimuli, leading to cell penetration of the nanoprobes as well as fluorescence restoration and visualization within the tumor cells. In this regard, the presented tumor-activatable and cell-permeable system deems to be an appealing platform to achieve selective tumor imaging and intracellular protein delivery. Its impact is therefore significant, far-reaching, and wide-spread.
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Affiliation(s)
- Lu Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Shuping Xie
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Jing Qi
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Ergang Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, PR China
| | - Di Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Quan Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, PR China
| | - Sunhui Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Huining He
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Victor C Yang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor Michigan 48109-1065, United States
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45
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Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB. Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites. Sci Rep 2017; 7:5755. [PMID: 28720874 PMCID: PMC5515926 DOI: 10.1038/s41598-017-06219-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/08/2017] [Indexed: 11/24/2022] Open
Abstract
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.
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Affiliation(s)
- Yanan Wang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jiangning Song
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana T Marquez-Lago
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - André Leier
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Chen Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
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Cieplak P, Strongin AY. Matrix metalloproteinases - From the cleavage data to the prediction tools and beyond. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1952-1963. [PMID: 28347746 DOI: 10.1016/j.bbamcr.2017.03.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/29/2022]
Abstract
Understanding the physiological role of any protease requires identification of both its cleavage substrates and their relative cleavage efficacy as compared with other substrates and other proteinases. Our review manuscript is focused on the cleavage preferences of the individual matrix metalloproteinases (MMPs) and the cleavage similarity and distinction that exist in the human MMP family. The recent in-depth analysis of MMPs by us and many others greatly increased knowledge of the MMP biology and structural-functional relationships among this protease family members. A better knowledge of cleavage preferences of MMPs has led us to the development of the prediction tools that are now capable of the high throughput reliable prediction and ranking the MMP cleavage sites in the peptide sequences in silico. Our software unifies and consolidates volumes of the pre-existing data. Now this prediction-ranking in silico tool is ready to be used by others. The software we developed may facilitate both the identification of the novel proteolytic regulatory pathways and the discovery of the previously uncharacterized substrates of the individual MMPs. Because now the MMP research may be based on the mathematical probability parameters rather than on either random luck or common sense alone, the researchers armed with this novel in silico tool will be better equipped to fine-tune or, at least, to sharply focus their wet chemistry experiments. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Piotr Cieplak
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.
| | - Alex Y Strongin
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.
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47
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Both Drosophila matrix metalloproteinases have released and membrane-tethered forms but have different substrates. Sci Rep 2017; 7:44560. [PMID: 28300207 PMCID: PMC5353688 DOI: 10.1038/srep44560] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/09/2017] [Indexed: 12/20/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are extracellular proteases that can cleave extracellular matrix and alter signaling pathways. They have been implicated in many disease states, but it has been difficult to understand the contribution of individual MMPs, as there are over 20 MMPs in vertebrates. The vertebrate MMPs have overlapping substrates, they exhibit genetic redundancy and compensation, and pharmacological inhibitors are non-specific. In contrast, there are only two MMP genes in Drosophila, DmMmp1 and DmMmp2, which makes Drosophila an attractive system to analyze the basis of MMP specificity. Previously, Drosophila MMPs have been categorized by their pericellular localization, as Mmp1 appeared to be secreted and Mmp2 appeared to be membrane-anchored, suggesting that protein localization was the critical distinction in this small MMP family. We report here that products of both genes are found at the cell surface and released into media. Additionally, we show that products of both genes contain GPI-anchors, and unexpectedly, that GPI-anchored MMPs promote cell adhesion when they are rendered inactive. Finally, by using new reagents and assays, we show that the two MMPs cleave different substrates, suggesting that this is the important distinction within this smallest MMP family.
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48
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Kasperkiewicz P, Poreba M, Groborz K, Drag M. Emerging challenges in the design of selective substrates, inhibitors and activity-based probes for indistinguishable proteases. FEBS J 2017; 284:1518-1539. [PMID: 28052575 PMCID: PMC7164106 DOI: 10.1111/febs.14001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/02/2016] [Accepted: 01/03/2017] [Indexed: 12/31/2022]
Abstract
Proteases are enzymes that hydrolyze the peptide bond of peptide substrates and proteins. Despite significant progress in recent years, one of the greatest challenges in the design and testing of substrates, inhibitors and activity‐based probes for proteolytic enzymes is achieving specificity toward only one enzyme. This specificity is particularly important if the enzyme is present with other enzymes with a similar catalytic mechanism and substrate specificity but completely different functionality. The cross‐reactivity of substrates, inhibitors and activity‐based probes with other enzymes can significantly impair or even prevent investigations of a target protease. In this review, we describe important concepts and the latest challenges, focusing mainly on peptide‐based substrate specificity techniques used to distinguish individual enzymes within major protease families.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
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49
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Fuchs JE, Schilling O, Liedl KR. Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. Curr Protein Pept Sci 2017; 18:905-913. [PMID: 27455965 PMCID: PMC5898033 DOI: 10.2174/1389203717666160724211231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/30/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. METHOD Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. RESULTS AND CONCLUSION We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
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Affiliation(s)
- Julian E. Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, D-79104 Freiburg, Germany and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104Freiburg, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020Innsbruck, Austria
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50
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Pethe MA, Rubenstein AB, Khare SD. Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design. J Mol Biol 2016; 429:220-236. [PMID: 27932294 DOI: 10.1016/j.jmb.2016.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022]
Abstract
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data. Here, we describe a general approach for predicting peptidase substrates de novo using protein structure modeling and biophysical evaluation of enzyme-substrate complexes. We construct atomic resolution models of thousands of candidate substrate-enzyme complexes for each of five model proteases belonging to the four major protease mechanistic classes-serine, cysteine, aspartyl, and metallo-proteases-and develop a discriminatory scoring function using enzyme design modules from Rosetta and AMBER's MMPBSA. We rank putative substrates based on calculated interaction energy with a modeled near-attack conformation of the enzyme active site. We show that the energetic patterns obtained from these simulations can be used to robustly rank and classify known cleaved and uncleaved peptides and that these structural-energetic patterns have greater discriminatory power compared to purely sequence-based statistical inference. Combining sequence and energetic patterns using machine-learning algorithms further improves classification performance, and analysis of structural models provides physical insight into the structural basis for the observed specificities. We further tested the predictive capability of the model by designing and experimentally characterizing the cleavage of four novel substrate motifs for the hepatitis C virus NS3/4 protease using an in vivo assay. The presented structure-based approach is generalizable to other protease enzymes with known or modeled structures, and complements existing experimental methods for specificity determination.
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Affiliation(s)
- Manasi A Pethe
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Aliza B Rubenstein
- Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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