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Bedian V, Biris N, Omer C, Chung JK, Fuller J, Dagher R, Chandran S, Harwin P, Kiselak T, Violin J, Nichols A, Bista P. STAR-0215 is a Novel, Long-Acting Monoclonal Antibody Inhibitor of Plasma Kallikrein for the Potential Treatment of Hereditary Angioedema. J Pharmacol Exp Ther 2023; 387:214-225. [PMID: 37643795 DOI: 10.1124/jpet.123.001740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Hereditary angioedema (HAE) is a rare autosomal dominant disorder caused by a deficiency in functional C1 esterase inhibitor, a serpin family protein that blocks the activity of plasma kallikrein. Insufficient inhibition of plasma kallikrein results in the overproduction of bradykinin, a vasoactive inflammatory mediator that produces both pain and unpredictable swelling during HAE attacks, with potentially life-threatening consequences. We describe the generation of STAR-0215, a humanized IgG1 antibody with a long circulating half-life (t1/2) that potently inhibits plasma kallikrein activity, with a >1000-fold lower affinity for prekallikrein and no measurable inhibitory activity against other serine proteases. The high specificity and inhibitory effect of STAR-0215 is demonstrated through a unique allosteric mechanism involving N-terminal catalytic domain binding, destabilization of the activation domain, and reversion of the active site to the inactive zymogen state. The YTE (M252Y/S254T/T256E) modified fragment crystallizable (Fc) domain of STAR-0215 enhances pH-dependent neonatal Fc receptor binding, resulting in a prolonged t1/2 in vivo (∼34 days in cynomolgus monkeys) compared with antibodies without this modification. A single subcutaneous dose of STAR-0215 (≥100 mg) was predicted to be active in patients for 3 months or longer, based on simulations using a minimal physiologically based pharmacokinetic model. These data indicate that STAR-0215, a highly potent and specific antibody against plasma kallikrein with extended t1/2, is a potential agent for long-term preventative HAE therapy administered every 3 months or less frequently. SIGNIFICANCE STATEMENT: STAR-0215 is a YTE-modified immunoglobulin G1 monoclonal antibody with a novel binding mechanism that specifically and potently inhibits the enzymatic activity of plasma kallikrein and prevents the generation of bradykinin. It has been designed to be a long-lasting prophylactic treatment to prevent attacks of HAE and to decrease the burden of disease and the burden of treatment for people with HAE.
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Affiliation(s)
- Vahe Bedian
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Nikolaos Biris
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Charles Omer
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Jou-Ku Chung
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - James Fuller
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Rafif Dagher
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Sachin Chandran
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Peter Harwin
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Tomas Kiselak
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Jonathan Violin
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Andrew Nichols
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
| | - Pradeep Bista
- Quellis Biosciences, Waltham, Massachusetts (V.B., C.O., P.H., T.K., J.V.); Astria Therapeutics, Inc., Boston, Massachusetts (N.B., C.O., J.K.C., R.D., S.C., J.V., A.N., P.B.); and Helix Biostructures, Indianapolis, Indiana (J.F.)
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2
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Kim S. TMPRSS4, a type II transmembrane serine protease, as a potential therapeutic target in cancer. Exp Mol Med 2023; 55:716-724. [PMID: 37009799 PMCID: PMC10167312 DOI: 10.1038/s12276-023-00975-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 04/04/2023] Open
Abstract
Proteases are involved in almost all biological processes, implying their importance for both health and pathological conditions. Dysregulation of proteases is a key event in cancer. Initially, research identified their role in invasion and metastasis, but more recent studies have shown that proteases are involved in all stages of cancer development and progression, both directly through proteolytic activity and indirectly via regulation of cellular signaling and functions. Over the past two decades, a novel subfamily of serine proteases called type II transmembrane serine proteases (TTSPs) has been identified. Many TTSPs are overexpressed by a variety of tumors and are potential novel markers of tumor development and progression; these TTSPs are possible molecular targets for anticancer therapeutics. The transmembrane protease serine 4 (TMPRSS4), a member of the TTSP family, is upregulated in pancreatic, colorectal, gastric, lung, thyroid, prostate, and several other cancers; indeed, elevated expression of TMPRSS4 often correlates with poor prognosis. Based on its broad expression profile in cancer, TMPRSS4 has been the focus of attention in anticancer research. This review summarizes up-to-date information regarding the expression, regulation, and clinical relevance of TMPRSS4, as well as its role in pathological contexts, particularly in cancer. It also provides a general overview of epithelial-mesenchymal transition and TTSPs.
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Affiliation(s)
- Semi Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, Korea.
- Department of Functional Genomics, Korea University of Science and Technology, Daejon, 34113, Korea.
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3
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Yu CC, Raj N, Chu JW. Statistical Learning of Protein Elastic Network from Positional Covariance Matrix. Comput Struct Biotechnol J 2023; 21:2524-2535. [PMID: 37095762 PMCID: PMC10121796 DOI: 10.1016/j.csbj.2023.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Positional fluctuation and covariance during protein dynamics are key observables for understanding the molecular origin of biological functions. A frequently employed potential energy function for describing protein structural variation at the coarse-gained level is elastic network model (ENM). A long-standing issue in biomolecular simulation is thus the parametrization of ENM spring constants from the components of positional covariance matrix (PCM). Based on sensitivity analysis of PCM, the direct-coupling statistics of each spring, which is a specific combination of position fluctuation and covariance, is found to exhibit prominent signal of parameter dependence. This finding provides the basis for devising the objective function and the scheme of running through the effective one-dimensional optimization of every spring by self-consistent iteration. Formal derivation of the positional covariance statistical learning (PCSL) method also motivates the necessary data regularization for stable calculations. Robust convergence of PCSL is achieved in taking an all-atom molecular dynamics trajectory or an ensemble of homologous structures as input data. The PCSL framework can also be generalized with mixed objective functions to capture specific property such as the residue flexibility profile. Such physical chemistry-based statistical learning thus provides a useful platform for integrating the mechanical information encoded in various experimental or computational data.
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4
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Zhou Y, Yu S, Chen D, Li H, Xu P, Yuan C, Jiang L, Huang M. Nafamostat Mesylate in Combination with the Mouse Amino-Terminal Fragment of Urokinase-Human Serum Albumin Improves the Treatment Outcome of Triple-Negative Breast Cancer Therapy. Mol Pharm 2023; 20:905-917. [PMID: 36463525 DOI: 10.1021/acs.molpharmaceut.2c00297] [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: 12/07/2022]
Abstract
Triple-negative breast cancer (TNBC) is highly aggressive and causes a higher proportion of metastatic cases. However, therapies directed to specific molecular targets have rarely achieved clinically meaningful improvements in the outcome of TNBC therapy. A urokinase-type plasminogen activator (uPA), one of the best-validated biomarkers of breast cancer, is an extracellular proteolytic serine protease involved in many pathological and physiological processes, including tumor cell invasion and metastasis. Nafamostat mesylate (NM) is a synthetic compound that inhibits various serine proteases and has been used as a therapeutic agent for the treatment of TNBC. Nevertheless, NM has poor specificity for serine proteases and is easy be hydrolyzed; moreover, the inhibitory mechanism of TNBC therapy is unclear. In this study, we combine NM with a macromolecular drug delivery vehicle, mouse amino-terminal fragment of urokinase-human serum albumin (mATF-HSA), to form a complex (mATF-HSA:NM) using the dilution-incubation-purification method. mATF specifically targets uPAR overexpressed on the surface of TNBC cells; moreover, HSA prevents NM from being hydrolyzed by numerous serine proteases. mATF-HSA:NM showed stronger inhibitory effects on the proliferation and metastasis of TNBC in vitro and in vivo without significant cytotoxicity on normal cells and tissues. In addition, we demonstrated that NM mediates metastasis of TNBC cells through inhibition of uPA using a stable uPA knockdown cell line (MDA-MB231 shuPA). Overall, we have developed a macromolecular complex targeted to treat high uPAR-expressing tumor types, and mATF-HSA can potentially be used to load other types of drugs with tumor-targeting specificity for mouse tumor models and is a promising tool to study tumor biology in mouse tumor models.
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Affiliation(s)
- Yang Zhou
- College of Chemistry, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Shujuan Yu
- College of Chemistry, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Dan Chen
- College of Chemistry, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Hanlin Li
- College of Chemistry, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Peng Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian350116, P.R. China.,Fujian Key Lab Moratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian350116, P.R. China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian350116, P.R. China
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5
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Gerhardy S, Ultsch M, Tang W, Green E, Holden JK, Li W, Estevez A, Arthur C, Tom I, Rohou A, Kirchhofer D. Allosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration. Nat Commun 2022; 13:5222. [PMID: 36064790 PMCID: PMC9445180 DOI: 10.1038/s41467-022-32760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric inhibition mechanism of HTRA1 by a clinical Fab fragment, currently being evaluated for GA treatment. Using cryo-EM, X-ray crystallography and biochemical assays we identify the exposed LoopA of HTRA1 as the sole Fab epitope, which is approximately 30 Å away from the active site. The cryo-EM structure of the HTRA1:Fab complex in combination with molecular dynamics simulations revealed that Fab binding to LoopA locks HTRA1 in a non-competent conformational state, incapable of supporting catalysis. Moreover, grafting the HTRA1-LoopA epitope onto HTRA2 and HTRA3 transferred the allosteric inhibition mechanism. This suggests a conserved conformational lock mechanism across the HTRA family and a critical role of LoopA for catalysis, which was supported by the reduced activity of HTRA1-3 upon LoopA deletion or perturbation. This study reveals the long-range inhibition mechanism of the clinical Fab and identifies an essential function of the exposed LoopA for activity of HTRA family proteases.
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Affiliation(s)
- Stefan Gerhardy
- Department of Early Discovery Biochemistry, Genentech Inc., San Francisco, CA, USA
| | - Mark Ultsch
- Department of Structural Biology, Genentech Inc., San Francisco, CA, USA
| | - Wanjian Tang
- Department of Early Discovery Biochemistry, Genentech Inc., San Francisco, CA, USA
| | - Evan Green
- Department of Structural Biology, Genentech Inc., San Francisco, CA, USA
| | - Jeffrey K Holden
- Department of Early Discovery Biochemistry, Genentech Inc., San Francisco, CA, USA
| | - Wei Li
- Department of Early Discovery Biochemistry, Genentech Inc., San Francisco, CA, USA
| | - Alberto Estevez
- Department of Structural Biology, Genentech Inc., San Francisco, CA, USA
| | - Chris Arthur
- Department of Structural Biology, Genentech Inc., San Francisco, CA, USA
| | - Irene Tom
- Department of OMNI Biomarker Development, Genentech Inc., San Francisco, CA, USA
| | - Alexis Rohou
- Department of Structural Biology, Genentech Inc., San Francisco, CA, USA
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech Inc., San Francisco, CA, USA.
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6
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Gomes PS, Carneiro MPD, Machado PDA, de Andrade-Neto VV, da Fonseca-Martins AM, Goundry A, Pereira da Silva JVM, Gomes DCO, Lima APCDA, Ennes-Vidal V, Sodero ACR, De-Simone SG, de Matos Guedes HL. Subtilisin of Leishmania amazonensis as Potential Druggable Target: Subcellular Localization, In Vitro Leishmanicidal Activity and Molecular Docking of PF-429242, a Subtilisin Inhibitor. Curr Issues Mol Biol 2022; 44:2089-2106. [PMID: 35678670 PMCID: PMC9164065 DOI: 10.3390/cimb44050141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
Subtilisin proteases, found in all organisms, are enzymes important in the post-translational steps of protein processing. In Leishmania major and L. donovani, this enzyme has been described as essential to their survival; however, few compounds that target subtilisin have been investigated for their potential as an antileishmanial drug. In this study, we first show, by electron microscopy and flow cytometry, that subtilisin has broad localization throughout the cytoplasm and membrane of the parasite in the promastigote form with foci in the flagellar pocket. Through in silico analysis, the similarity between subtilisin of different Leishmania species and that of humans were determined, and based on molecular docking, we evaluated the interaction capacity of a serine protease inhibitor against both life cycle forms of Leishmania. The selected inhibitor, known as PF-429242, has already been used against the dengue virus, arenaviruses, and the hepatitis C virus. Moreover, it proved to have antilipogenic activity in a mouse model and caused hypolipidemia in human cells in vitro. Here, PF-429242 significantly inhibited the growth of L. amazonensis promastigotes of four different strains (IC50 values = 3.07 ± 0.20; 0.83 ± 0.12; 2.02 ± 0.27 and 5.83 ± 1.2 µM against LTB0016, PH8, Josefa and LV78 strains) whilst having low toxicity in the host macrophages (CC50 = 170.30 µM). We detected by flow cytometry that there is a greater expression of subtilisin in the amastigote form; however, PF-429242 had a low effect against this intracellular form with an IC50 of >100 µM for intracellular amastigotes, as well as against axenic amastigotes (94.12 ± 2.8 µM for the LV78 strain). In conclusion, even though PF-429242 does not affect the intracellular forms, this drug will serve as a tool to explore pharmacological and potentially leishmanicidal targets.
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Affiliation(s)
- Pollyanna Stephanie Gomes
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Monique Pacheco Duarte Carneiro
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (A.G.); (A.P.C.d.A.L.)
| | - Patrícia de Almeida Machado
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Valter Viana de Andrade-Neto
- Laboratório de Bioquímica de Tripanossomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil;
| | - Alessandra Marcia da Fonseca-Martins
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Amy Goundry
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (A.G.); (A.P.C.d.A.L.)
| | | | | | - Ana Paula Cabral de Araujo Lima
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (A.G.); (A.P.C.d.A.L.)
| | - Vítor Ennes-Vidal
- Laboratório de Estudos Integrados em Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil;
| | - Ana Carolina Rennó Sodero
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.V.M.P.d.S.); (A.C.R.S.)
| | - Salvatore Giovanni De-Simone
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Diseases Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
- Epidemiology and Molecular Systematic Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Cellular and Molecular Biology Department, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
| | - Herbert L. de Matos Guedes
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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7
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Sorensen AB, Greisen PJ, Madsen JJ, Lund J, Andersen G, Wulff-Larsen PG, Pedersen AA, Gandhi PS, Overgaard MT, Østergaard H, Olsen OH. A systematic approach for evaluating the role of surface-exposed loops in trypsin-like serine proteases applied to the 170 loop in coagulation factor VIIa. Sci Rep 2022; 12:3747. [PMID: 35260627 PMCID: PMC8904457 DOI: 10.1038/s41598-022-07620-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
Proteases play a major role in many vital physiological processes. Trypsin-like serine proteases (TLPs), in particular, are paramount in proteolytic cascade systems such as blood coagulation and complement activation. The structural topology of TLPs is highly conserved, with the trypsin fold comprising two β-barrels connected by a number of variable surface-exposed loops that provide a surprising capacity for functional diversity and substrate specificity. To expand our understanding of the roles these loops play in substrate and co-factor interactions, we employ a systematic methodology akin to the natural truncations and insertions observed through evolution of TLPs. The approach explores a larger deletion space than classical random or directed mutagenesis. Using FVIIa as a model system, deletions of 1–7 amino acids through the surface exposed 170 loop, a vital allosteric regulator, was introduced. All variants were extensively evaluated by established functional assays and computational loop modelling with Rosetta. The approach revealed detailed structural and functional insights recapitulation and expanding on the main findings in relation to 170 loop functions elucidated over several decades using more cumbersome crystallization and single deletion/mutation methodologies. The larger deletion space was key in capturing the most active variant, which unexpectedly had a six-amino acid truncation. This variant would have remained undiscovered if only 2–3 deletions were considered, supporting the usefulness of the methodology in general protease engineering approaches. Our findings shed further light on the complex role that surface-exposed loops play in TLP function and supports the important role of loop length in the regulation and fine-tunning of enzymatic function throughout evolution.
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Affiliation(s)
- Anders B Sorensen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark.,Department of Chemistry and Bioscience, Aalborg University, 9220, Ålborg, Denmark
| | | | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Jacob Lund
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Gorm Andersen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | | | | | | | - Michael T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, 9220, Ålborg, Denmark
| | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark. .,Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
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8
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Naeem M, Manzoor S, Abid MUH, Tareen MBK, Asad M, Mushtaq S, Ehsan N, Amna D, Xu B, Hazafa A. Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review. J Fungi (Basel) 2022; 8:jof8020109. [PMID: 35205863 PMCID: PMC8875690 DOI: 10.3390/jof8020109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.
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Affiliation(s)
- Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang 050025, China;
| | - Saba Manzoor
- Department of Zoology, University of Sialkot, Sialkot 51310, Pakistan;
| | | | | | - Mirza Asad
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot 51040, Pakistan;
| | - Nazia Ehsan
- Department of Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Dua Amna
- Institute of Food Science & Nutrition, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University (BNU-HKBU) United International College, Zhuhai 519087, China
- Correspondence: (B.X.); (A.H.)
| | - Abu Hazafa
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
- Correspondence: (B.X.); (A.H.)
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Tatarko M, Ivanov IN, Hianik T. New Insights on Plasmin Long Term Stability and the Mechanism of Its Activity Inhibition Analyzed by Quartz Crystal Microbalance. MICROMACHINES 2021; 13:mi13010055. [PMID: 35056220 PMCID: PMC8777901 DOI: 10.3390/mi13010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 12/04/2022]
Abstract
We used the research quartz crystal microbalance (RQCM) to monitor regulatory effects of plasmin and trypsin in the presence of their inhibitor α2-antiplasmin. The gold surface of quartz crystals was modified with a β-casein layer that served as a substrate for protease digestion. The addition of plasmin or trypsin as well as their mixtures with α2-antiplasmin resulted in an increase of resonant frequency, f, and in a decrease of motional resistance, Rm, depending on the molar ratio of protease: antiplasmin. At equimolar concentrations of protease and α2-antiplasmin (5 nM:5 nM) full inhibition of protease activity took place. Monitoring of plasmin activity on an hourly and daily basis revealed a prominent effect of autolysis and decrease of plasmin activity in freshly activated samples. The degree of inhibition as well as plasmin half-life (t1/2 = 2.48 ± 0.28 days) connected with its degradation was determined.
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Affiliation(s)
- Marek Tatarko
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina, 842 48 Bratislava, Slovakia;
| | - Ilia N. Ivanov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6496, USA;
| | - Tibor Hianik
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina, 842 48 Bratislava, Slovakia;
- Correspondence:
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Structural and functional significance of the amino acid differences Val 35Thr, Ser 46Ala, Asn 65Ser, and Ala 94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Int J Biol Macromol 2021; 193:2113-2120. [PMID: 34774600 PMCID: PMC8580570 DOI: 10.1016/j.ijbiomac.2021.11.043] [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: 09/04/2021] [Revised: 10/07/2021] [Accepted: 11/05/2021] [Indexed: 11/28/2022]
Abstract
Three dimensional structures of (chymo)trypsin-like proteinase (3CLpro) from SARS-CoV-2 and SARS-CoV differ at 8 positions. We previously found that the Val86Leu, Lys88Arg, Phe134His, and Asn180Lys mutations in these enzymes can change the orientation of the N- and C-terminal domains of 3CLpro relative to each other, which leads to a change in catalytic activity. This conclusion was derived from the comparison of the structural catalytic core in 169 (chymo)trypsin-like proteinases with the serine/cysteine fold. Val35Thr, Ser46Ala, Asn65Ser, Ala94Ser mutations were not included in that analysis, since they are located far from the catalytic tetrad. In the present work, the structural and functional roles of these variable amino acids at positions 35, 46, 65, and 94 in the 3CLpro sequences of SARS-CoV-2 and SARS-CoV have been established using a comparison of the same set of proteinases leading to the identification of new conservative elements. Comparative analysis showed that, in addition to interdomain mobility, which could modulate catalytic activity, the 3CLpro(s) can use for functional regulation an autolytic loop and the unique Asp33-Asn95 region (the Asp33-Asn95 Zone) in the N-terminal domain. Therefore, all 4 analyzed mutation sites are associated with the unique structure-functional features of the 3CLpro from SARS-CoV-2 and SARS-CoV. Strictly speaking, the presented structural results are hypothetical, since at present there is not a single experimental work on the identification and characterization of autolysis sites in these proteases.
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11
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Structural basis of covalent inhibitory mechanism of TMPRSS2-related serine proteases by camostat. J Virol 2021; 95:e0086121. [PMID: 34160253 PMCID: PMC8428381 DOI: 10.1128/jvi.00861-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen causing the coronavirus disease 2019 (COVID-19) global pandemic. No effective treatment for COVID-19 has been established yet. The serine protease transmembrane protease serine 2 (TMPRSS2) is essential for viral spread and pathogenicity by facilitating the entry of SARS-CoV-2 into host cells. The protease inhibitor camostat, an anticoagulant used in the clinic, has potential anti-inflammatory and antiviral activities against COVID-19. However, the potential mechanisms of viral resistance and antiviral activity of camostat are unclear. Herein, we demonstrate high inhibitory potencies of camostat for a panel of serine proteases, indicating that camostat is a broad-spectrum inhibitor of serine proteases. In addition, we determined the crystal structure of camostat in complex with a serine protease (uPA [urokinase-type plasminogen activator]), which reveals that camostat is inserted in the S1 pocket of uPA but is hydrolyzed by uPA, and the cleaved camostat covalently binds to Ser195. We also generated a homology model of the structure of the TMPRSS2 serine protease domain. The model shows that camostat uses the same inhibitory mechanism to inhibit the activity of TMPRSS2, subsequently preventing SARS-CoV-2 spread. IMPORTANCE Serine proteases are a large family of enzymes critical for multiple physiological processes and proven diagnostic and therapeutic targets in several clinical indications. The serine protease transmembrane protease serine 2 (TMPRSS2) was recently found to mediate SARS-CoV-2 entry into the host. Camostat mesylate (FOY 305), a serine protease inhibitor active against TMPRSS2 and used for the treatment of oral squamous cell carcinoma and chronic pancreatitis, inhibits SARS-CoV-2 infection of human lung cells. However, the direct inhibition mechanism of camostat mesylate for TMPRSS2 is unclear. Herein, we demonstrate that camostat uses the same inhibitory mechanism to inhibit the activity of TMPRSS2 as uPA, subsequently preventing SARS-CoV-2 spread.
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