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Davoine C, Traina A, Evrard J, Lanners S, Fillet M, Pochet L. Coumarins as factor XIIa inhibitors: Potency and selectivity improvements using a fragment-based strategy. Eur J Med Chem 2023; 259:115636. [PMID: 37478556 DOI: 10.1016/j.ejmech.2023.115636] [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: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Previously, we described weak coumarin inhibitors of factor XIIa, a promising target for artificial surface-induced thrombosis and various inflammatory diseases. In this work, we used fragment-based drug discovery approach to improve our coumarin series. First, we screened about 200 fragments for the S1 pocket. The S1 pocket of trypsin-like serine proteases, such as factor XIIa, is highly conserved and is known to drive a major part of the association energy. From the screening, we selected fragments displaying a micromolar activity and studied their selectivity on other serine proteases. Then, these fragments were merged to our coumarin templates, leading to the generation of nanomolar inhibitors. The mechanism of inhibition was further studied by mass spectrometry demonstrating the covalent binding through the formation of an acyl enzyme complex. The most potent compound was tested in plasma to evaluate its stability and efficacy on coagulation assays. It exhibited a plasmatic half-life of 1.9 h and a good selectivity for the intrinsic coagulation pathway over the extrinsic one.
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Affiliation(s)
- Clara Davoine
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium; Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Place Du 20 Août 7, 4000, Liège, Belgium
| | - Amandine Traina
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Jonathan Evrard
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Steve Lanners
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Place Du 20 Août 7, 4000, Liège, Belgium
| | - Lionel Pochet
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium.
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2
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Siow A, Kowalczyk R, Brimble MA, Harris PWR. Evolution of Peptide-Based Prostate-Specific Membrane Antigen (PSMA) Inhibitors: An Approach to Novel Prostate Cancer Therapeutics. Curr Med Chem 2021; 28:3713-3752. [PMID: 33023429 DOI: 10.2174/0929867327666201006153847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Prostate cancer is one of the most common cancers worldwide, with approximately 1.1 million cases diagnosed annually. The rapid development of molecular imaging has facilitated greater structural understanding, which can help formulate novel combinations of therapeutic regimens and more accurate diagnosis, avoiding unnecessary prostate biopsies. This accumulated knowledge also provides a greater understanding of the aggressive stages of the disease and tumor recurrence. Recently, much progress has been made on developing peptidomimetic-based inhibitors as promising candidates to effectively bind to the prostate- specific membrane antigen (PSMA), which is expressed by prostate cancer cells. OBJECTIVE In this review, recent advances covering small-molecule and peptide-based PSMA inhibitors will be extensively reviewed, providing a base for the rational design of future PSMA inhibitors. METHOD Herein, the literature on selected PSMA inhibitors that have been developed from 1996 to 2020 were reviewed, emphasizing recent synthetic advances and chemical strategies whilst highlighting therapeutic potential and drawbacks of each inhibitor. RESULTS Synthesized inhibitors presented in this review demonstrate the clinical application of certain PSMA inhibitors, exhibited in vitro and in vivo. CONCLUSION This review highlights the clinical potential of PSMA inhibitors, analyzing the advantages and setbacks of the chemical synthetic methodologies utilized, setting precedence for the discovery of novel PSMA inhibitors for future clinical applications.
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Affiliation(s)
- Andrew Siow
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Private Bag: 92019, Auckland 1010, New Zealand
| | - Renata Kowalczyk
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Private Bag: 92019, Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Private Bag: 92019, Auckland 1010, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Private Bag: 92019, Auckland 1010, New Zealand
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3
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Fuentes-Prior P. Priming of SARS-CoV-2 S protein by several membrane-bound serine proteinases could explain enhanced viral infectivity and systemic COVID-19 infection. J Biol Chem 2020; 296:100135. [PMID: 33268377 PMCID: PMC7834812 DOI: 10.1074/jbc.rev120.015980] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
The ongoing COVID-19 pandemic has already caused over a million deaths worldwide, and this death toll will be much higher before effective treatments and vaccines are available. The causative agent of the disease, the coronavirus SARS-CoV-2, shows important similarities with the previously emerged SARS-CoV-1, but also striking differences. First, SARS-CoV-2 possesses a significantly higher transmission rate and infectivity than SARS-CoV-1 and has infected in a few months over 60 million people. Moreover, COVID-19 has a systemic character, as in addition to the lungs, it also affects the heart, liver, and kidneys among other organs of the patients and causes frequent thrombotic and neurological complications. In fact, the term "viral sepsis" has been recently coined to describe the clinical observations. Here I review current structure-function information on the viral spike proteins and the membrane fusion process to provide plausible explanations for these observations. I hypothesize that several membrane-associated serine proteinases (MASPs), in synergy with or in place of TMPRSS2, contribute to activate the SARS-CoV-2 spike protein. Relative concentrations of the attachment receptor, ACE2, MASPs, their endogenous inhibitors (the Kunitz-type transmembrane inhibitors, HAI-1/SPINT1 and HAI-2/SPINT2, as well as major circulating serpins) would determine the infection rate of host cells. The exclusive or predominant expression of major MASPs in specific human organs suggests a direct role of these proteinases in e.g., heart infection and myocardial injury, liver dysfunction, kidney damage, as well as neurological complications. Thorough consideration of these factors could have a positive impact on the control of the current COVID-19 pandemic.
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Affiliation(s)
- Pablo Fuentes-Prior
- Molecular Bases of Disease, Biomedical Research Institute (IIB) Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
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4
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Kwon H, Ha H, Jeon H, Jang J, Son SH, Lee K, Park SK, Byun Y. Structure-activity relationship studies of dipeptide-based hepsin inhibitors with Arg bioisosteres. Bioorg Chem 2020; 107:104521. [PMID: 33334587 DOI: 10.1016/j.bioorg.2020.104521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/09/2023]
Abstract
Hepsin is a type II transmembrane serine protease (TTSP) associated with cell proliferation and overexpressed in several types of cancer including prostate cancer (PCa). Because of its significant role in cancer progression and metastasis, hepsin is an attractive protein as a potential therapeutic and diagnostic biomarker for PCa. Based on the reported Leu-Arg dipeptide-based hepsin inhibitors, we performed structural modification and determined in vitro hepsin- and matriptase-inhibitory activities. Comprehensive structure-activity relationship studies identified that the p-guanidinophenylalanine-based dipeptide analog 22a exhibited a strong hepsin-inhibitory activity (Ki = 50.5 nM) and 22-fold hepsin selectivity over matriptase. Compound 22a could be a prototype molecule for structural optimization of dipeptide-based hepsin inhibitors.
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Affiliation(s)
- Hongmok Kwon
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Hyunsoo Ha
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Hayoung Jeon
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Jaebong Jang
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Sang-Hyun Son
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Kiho Lee
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Song-Kyu Park
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Youngjoo Byun
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea; Biomedical Research Center, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea.
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5
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Huggins DJ. Structural analysis of experimental drugs binding to the SARS-CoV-2 target TMPRSS2. J Mol Graph Model 2020; 100:107710. [PMID: 32829149 PMCID: PMC7417922 DOI: 10.1016/j.jmgm.2020.107710] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022]
Abstract
The emergence of SARS-CoV-2 has prompted a worldwide health emergency. There is an urgent need for therapeutics, both through the repurposing of approved drugs and the development of new treatments. In addition to the viral drug targets, a number of human drug targets have been suggested. In theory, targeting human proteins should provide an advantage over targeting viral proteins in terms of drug resistance, which is commonly a problem in treating RNA viruses. This paper focuses on the human protein TMPRSS2, which supports coronavirus life cycles by cleaving viral spike proteins. The three-dimensional structure of TMPRSS2 is not known and so we have generated models of the TMPRSS2 in the apo state as well as in complex with a peptide substrate and putative inhibitors to aid future work. Importantly, many related human proteases have 80% or higher identity with TMPRSS2 in the S1-S1' subsites, with plasminogen and urokinase-type plasminogen activator (uPA) having 95% identity. We highlight 376 approved, investigational or experimental drugs targeting S1A serine proteases that may also inhibit TMPRSS2. Whilst the presence of a relatively uncommon lysine residue in the S2/S3 subsites means that some serine protease inhibitors will not inhibit TMPRSS2, this residue is likely to provide a handle for selective targeting in a focused drug discovery project. We discuss how experimental drugs targeting related serine proteases might be repurposed as TMPRSS2 inhibitors to treat coronaviruses.
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Affiliation(s)
- David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA.
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6
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Robson B. COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles' heel conserved region to minimize probability of escape mutations and drug resistance. Comput Biol Med 2020; 121:103749. [PMID: 32568687 PMCID: PMC7151553 DOI: 10.1016/j.compbiomed.2020.103749] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022]
Abstract
This paper continues a recent study of the spike protein sequence of the COVID-19 virus (SARS-CoV-2). It is also in part an introductory review to relevant computational techniques for tackling viral threats, using COVID-19 as an example. Q-UEL tools for facilitating access to knowledge and bioinformatics tools were again used for efficiency, but the focus in this paper is even more on the virus. Subsequence KRSFIEDLLFNKV of the S2′ spike glycoprotein proteolytic cleavage site continues to appear important. Here it is shown to be recognizable in the common cold coronaviruses, avian coronaviruses and possibly as traces in the nidoviruses of reptiles and fish. Its function or functions thus seem important to the coronaviruses. It might represent SARS-CoV-2 Achilles’ heel, less likely to acquire resistance by mutation, as has happened in some early SARS vaccine studies discussed in the previous paper. Preliminary conformational analysis of the receptor (ACE2) binding site of the spike protein is carried out suggesting that while it is somewhat conserved, it appears to be more variable than KRSFIEDLLFNKV. However compounds like emodin that inhibit SARS entry, apparently by binding ACE2, might also have functions at several different human protein binding sites. The enzyme 11β-hydroxysteroid dehydrogenase type 1 is again argued to be a convenient model pharmacophore perhaps representing an ensemble of targets, and it is noted that it occurs both in lung and alimentary tract. Perhaps it benefits the virus to block an inflammatory response by inhibiting the dehydrogenase, but a fairly complex web involves several possible targets. This paper “drills down” into the studies of the author's previous COVID-19 paper. Designing vaccine and drugs must seek to avoid escape mutations. Subsequence KRSFIEDLLFNKV seems recognizable across many coronaviruses. The ACE2 binding domain is a target, but shows variation. A steroid dehydrogenase is argued to remain an interesting model pharmacophore.
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Affiliation(s)
- B Robson
- Ingine Inc. Cleveland Ohio USA, The Dirac Foundation, Oxfordshire, UK.
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7
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Robson B. Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus. Comput Biol Med 2020; 119:103670. [PMID: 32209231 PMCID: PMC7094376 DOI: 10.1016/j.compbiomed.2020.103670] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/19/2022]
Abstract
This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic, and to explore some design possibilities. The project was originally directed towards a use case for the Q-UEL language and its implementation in a knowledge management and automated inference system for medicine called the BioIngine, but focus here remains mostly on the virus itself. However, using Q-UEL systems to access relevant and emerging literature, and to interact with standard publically available bioinformatics tools on the Internet, did help quickly identify sequences of amino acids that are well conserved across many coronaviruses including 2019-nCoV. KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry. This sequence motif and surrounding variations formed the basis for proposing a specific synthetic vaccine epitope and peptidomimetic agent. The work can, nonetheless, be described in traditional bioinformatics terms, and readily reproduced by others, albeit with the caveat that new data and research into 2019-nCoV is emerging and evolving at an explosive pace. Preliminary studies using molecular modeling and docking, and in that context the potential value of certain known herbal extracts, are also described. Bioinformatics studies are carried out on the COVID-19 virus. A sequence motif KRSFIEDLLFNKV is of particular interest. Based on the above, synthetic peptides are designed. Preliminary considerations are also given to non-peptide organic molecules.
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Affiliation(s)
- B Robson
- Ingine Inc., Cleveland, Ohio, USA; The Dirac Foundation, Oxfordshire, UK.
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8
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Kim K, Kwon H, Choi D, Lim T, Minn I, Son SH, Byun Y. Design and synthesis of dye-conjugated hepsin inhibitors. Bioorg Chem 2019; 89:102990. [DOI: 10.1016/j.bioorg.2019.102990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 01/28/2023]
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9
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Mican J, Toul M, Bednar D, Damborsky J. Structural Biology and Protein Engineering of Thrombolytics. Comput Struct Biotechnol J 2019; 17:917-938. [PMID: 31360331 PMCID: PMC6637190 DOI: 10.1016/j.csbj.2019.06.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 12/22/2022] Open
Abstract
Myocardial infarction and ischemic stroke are the most frequent causes of death or disability worldwide. Due to their ability to dissolve blood clots, the thrombolytics are frequently used for their treatment. Improving the effectiveness of thrombolytics for clinical uses is of great interest. The knowledge of the multiple roles of the endogenous thrombolytics and the fibrinolytic system grows continuously. The effects of thrombolytics on the alteration of the nervous system and the regulation of the cell migration offer promising novel uses for treating neurodegenerative disorders or targeting cancer metastasis. However, secondary activities of thrombolytics may lead to life-threatening side-effects such as intracranial bleeding and neurotoxicity. Here we provide a structural biology perspective on various thrombolytic enzymes and their key properties: (i) effectiveness of clot lysis, (ii) affinity and specificity towards fibrin, (iii) biological half-life, (iv) mechanisms of activation/inhibition, and (v) risks of side effects. This information needs to be carefully considered while establishing protein engineering strategies aiming at the development of novel thrombolytics. Current trends and perspectives are discussed, including the screening for novel enzymes and small molecules, the enhancement of fibrin specificity by protein engineering, the suppression of interactions with native receptors, liposomal encapsulation and targeted release, the application of adjuvants, and the development of improved production systems.
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Key Words
- EGF, Epidermal growth factor domain
- F, Fibrin binding finger domain
- Fibrinolysis
- K, Kringle domain
- LRP1, Low-density lipoprotein receptor-related protein 1
- MR, Mannose receptor
- NMDAR, N-methyl-D-aspartate receptor
- P, Proteolytic domain
- PAI-1, Inhibitor of tissue plasminogen activator
- Plg, Plasminogen
- Plm, Plasmin
- RAP, Receptor antagonist protein
- SAK, Staphylokinase
- SK, Streptokinase
- Staphylokinase
- Streptokinase
- Thrombolysis
- Tissue plasminogen activator
- Urokinase
- t-PA, Tissue plasminogen activator
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Affiliation(s)
- Jan Mican
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Toul
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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Wang D, Yang Y, Jiang L, Wang Y, Li J, Andreasen PA, Chen Z, Huang M, Xu P. Suppression of Tumor Growth and Metastases by Targeted Intervention in Urokinase Activity with Cyclic Peptides. J Med Chem 2019; 62:2172-2183. [PMID: 30707839 DOI: 10.1021/acs.jmedchem.8b01908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Urokinase-type plasminogen activator (uPA) is a diagnostic marker for breast and prostate cancers recommended by American Society for Clinical Oncology and German Breast Cancer Society. Inhibition of uPA was proposed as an efficient strategy for cancer treatments. In this study, we report peptide-based uPA inhibitors with high potency and specificity comparable to monoclonal antibodies. We revealed the binding and inhibitory mechanisms by combining crystallography, molecular dynamic simulation, and other biophysical and biochemical approaches. Besides, we showed that our peptides efficiently inhibited the invasion of cancer cells via intervening with the processes of the degradation of extracellular matrices. Furthermore, our peptides significantly suppressed the tumor growth and the cancer metastases in tumor-bearing mice. This study demonstrates that these uPA peptides are highly potent anticancer agents and reveals the mechanistic insights of these uPA inhibitors, which can be useful for developing other serine protease inhibitors.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,University of Chinese Academy of Sciences , No.19 (A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Yongshuai Yang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,University of Chinese Academy of Sciences , No.19 (A) Yuquan Road , Shijingshan District, Beijing 100049 , China.,College of Life Science , Fujian Agriculture and Forestry University , Fuzhou , Fujian 350002 , China
| | - Longguang Jiang
- College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Yu Wang
- College of Life Science , Fujian Agriculture and Forestry University , Fuzhou , Fujian 350002 , China
| | - Jinyu Li
- College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics , Aarhus University , Aarhus C 8000 , Denmark
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Peng Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China
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11
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El-Sharief MAMS, El-Naggar MH, Ahmed EM, El-Messery SM, Mahmoud AE, Ali MM, Salem LM, Mahrous KF, El Sayed MT. Tetrahydroindolocarbazoles (THICZs) as new class of urokinase (uPA) inhibitors: Synthesis, anticancer evaluation, DNA-damage determination, and molecular modelling study. Bioorg Chem 2018; 80:545-554. [PMID: 30014922 DOI: 10.1016/j.bioorg.2018.06.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/05/2018] [Accepted: 06/29/2018] [Indexed: 11/15/2022]
Abstract
Tetrahydroindolocarbazoles (THICZs) with versatile substituents, have been designed, synthesized, structure characterized, then investigated for their in-vitro anticancer screening, urokinase inhibition (uPA) evaluated, DNA-damage determination was further explored. Compounds 5, 8, 10 and 17 displayed the most promising antitumor activities against the breast cancer cell line as compared to the standard drug, doxorubicin with IC50 = 5.24 ± 0.37, 4.00 ± 0.52, 7.20 ± 0.90 and 9.60 ± 1.10 µg/ml (versus 3.30 ± 0.48 µg/ml for doxorubicin). Compounds 5, 8, 10 and 17 represents the most significant uPA inhibitors of our study with IC50 of 3.80, 2.70. 4.75, 10.80 (ng/ml) respectively. The expression levels of CDKN2A gene were decreased in 8, 10 and 17 cell lines as compared to those in positive control samples. Cell lines treated with 5, 8, 10 and 17 clearly observed a high score of damaged DNA cells. A deeper examination revealed that our hetroaromatics showed an extensive hydrogen bonding interactions that is required in the S pocket which is important for activity Arg 217, Gly 219, Gly 216, Lys 143 and Ser 190. So we present THICZs as promising uPA inhibitors expected as significant promise for further development as anti-invasiveness drugs.
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Affiliation(s)
- Marwa A M Sh El-Sharief
- Department of Applied Organic Chemistry, National Research Centre, 12622 Dokki, Giza, Egypt; Chemistry Department, Faculty of Sciences, King Khaled University, Saudi Arabia
| | - Mohamed H El-Naggar
- Chemistry Department, Faculty of Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Entesar M Ahmed
- Chemistry Department, Faculty of Science, Al Azhar University, Cairo, Egypt
| | - Shahenda M El-Messery
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt.
| | - Abeer E Mahmoud
- Biochemistry Department, Division of Genetic Engineering and Biotechnology, National Research Centre, Dokki 12622, Giza, Egypt
| | - Mamdouh M Ali
- Biochemistry Department, Division of Genetic Engineering and Biotechnology, National Research Centre, Dokki 12622, Giza, Egypt
| | - Lamiaa M Salem
- Cell Biology Department, National Research Centre, 12622-Dokki, Egypt
| | - Karima F Mahrous
- Cell Biology Department, National Research Centre, 12622-Dokki, Egypt
| | - Mardia T El Sayed
- Department of Applied Organic Chemistry, National Research Centre, 12622 Dokki, Giza, Egypt.
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12
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Solis-Calero C, Zanatta G, Pessoa CDÓ, Carvalho HF, Freire VN. Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry. Phys Chem Chem Phys 2018; 20:22818-22830. [DOI: 10.1039/c8cp04315a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.
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Affiliation(s)
- Christian Solis-Calero
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Geancarlo Zanatta
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
| | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology
- Federal University of Ceará
- 60430-270 Fortaleza
- Brazil
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Valder N. Freire
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
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13
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de Veer SJ, Ukolova SS, Munro CA, Swedberg JE, Buckle AM, Harris JM. Mechanism-based selection of a potent kallikrein-related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI-1. Biopolymers 2016; 100:510-8. [PMID: 24078181 DOI: 10.1002/bip.22231] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/01/2013] [Accepted: 03/02/2013] [Indexed: 02/06/2023]
Abstract
Potent and specific enzyme inhibition is a key goal in the development of therapeutic inhibitors targeting proteolytic activity. The backbone-cyclized peptide, Sunflower Trypsin Inhibitor (SFTI-1) affords a scaffold that can be engineered to achieve both these aims. SFTI-1's mechanism of inhibition is unusual in that it shows fast-on/slow-off kinetics driven by cleavage and religation of a scissile bond. This phenomenon was used to select a nanomolar inhibitor of kallikrein-related peptidase 7 (KLK7) from a versatile library of SFTI variants with diversity tailored to exploit distinctive surfaces present in the active site of serine proteases. Inhibitor selection was achieved through the use of size exclusion chromatography to separate protease/inhibitor complexes from unbound inhibitors followed by inhibitor identification according to molecular mass ascertained by mass spectrometry. This approach identified a single dominant inhibitor species with molecular weight of 1562.4 Da, which is consistent with the SFTI variant SFTI-WCTF. Once synthesized individually this inhibitor showed an IC50 of 173.9 ± 7.6 nM against chromogenic substrates and could block protein proteolysis. Molecular modeling analysis suggested that selection of SFTI-WCTF was driven by specific aromatic interactions and stabilized by an enhanced internal hydrogen bonding network. This approach provides a robust and rapid route to inhibitor selection and design.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
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14
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Subedi M, Minn I, Chen J, Kim Y, Ok K, Jung YW, Pomper MG, Byun Y. Design, synthesis and biological evaluation of PSMA/hepsin-targeted heterobivalent ligands. Eur J Med Chem 2016; 118:208-218. [PMID: 27128184 DOI: 10.1016/j.ejmech.2016.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/14/2016] [Accepted: 04/12/2016] [Indexed: 01/08/2023]
Abstract
Cell surface biomarkers such as prostate-specific membrane antigen (PSMA) and hepsin have received considerable attention as targets for imaging prostate cancer (PCa) due to their high cell surface expression in such tumors and easy access for imaging probes. Novel amidine-containing indole analogs (13-21) as hepsin inhibitors were designed and synthesized. These compounds showed in vitro inhibitory activity against hepsin with IC50 values from 5.9 to 70 μM. Based on the SAR of amidine-derived analogs, the novel heterobivalent compound 30, targeting both hepsin and PSMA, was synthesized by linking compound 18 with Lys-urea-Glu, the key scaffold for the specific binding to PSMA, followed by the conjugation of the optical dye SulfoCy7. Compound 30 exhibited inhibitory activities against PSMA and hepsin, with IC50 values of 28 nM and 2.8 μM, respectively. In vitro cell uptake and preliminary in vivo optical imaging studies of 30 showed selective binding and retention in both PSMA and hepsin high-expressing PC3/ML-PSMA-HPN cells as compared with low-expressing PC3/ML cells.
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Affiliation(s)
- Milan Subedi
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Il Minn
- Department of Radiology, Johns Hopkins Medical Institution, 1550 Orleans street, Baltimore 21287, MD, USA
| | - Jianbo Chen
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - YunHye Kim
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Kiwon Ok
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Yong Woo Jung
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Martin G Pomper
- Department of Radiology, Johns Hopkins Medical Institution, 1550 Orleans street, Baltimore 21287, MD, USA
| | - Youngjoo Byun
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea.,Department of Radiology, Johns Hopkins Medical Institution, 1550 Orleans street, Baltimore 21287, MD, USA.,Biomedical Research Center, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul 152-703, South Korea
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15
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Kwon H, Kim Y, Park K, Choi SA, Son SH, Byun Y. Structure-based design, synthesis, and biological evaluation of Leu-Arg dipeptide analogs as novel hepsin inhibitors. Bioorg Med Chem Lett 2016; 26:310-314. [DOI: 10.1016/j.bmcl.2015.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 12/11/2022]
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16
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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17
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Barré O, Dufour A, Eckhard U, Kappelhoff R, Béliveau F, Leduc R, Overall CM. Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs) using PICS with proteome-derived peptide libraries. PLoS One 2014; 9:e105984. [PMID: 25211023 PMCID: PMC4161349 DOI: 10.1371/journal.pone.0105984] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/31/2014] [Indexed: 01/08/2023] Open
Abstract
Background Type II transmembrane serine proteases (TTSPs) are a family of cell membrane tethered serine proteases with unclear roles as their cleavage site specificities and substrate degradomes have not been fully elucidated. Indeed just 52 cleavage sites are annotated in MEROPS, the database of proteases, their substrates and inhibitors. Methodology/Principal Finding To profile the active site specificities of the TTSPs, we applied Proteomic Identification of protease Cleavage Sites (PICS). Human proteome-derived database searchable peptide libraries were assayed with six human TTSPs (matriptase, matriptase-2, matriptase-3, HAT, DESC and hepsin) to simultaneously determine sequence preferences on the N-terminal non-prime (P) and C-terminal prime (P’) sides of the scissile bond. Prime-side cleavage products were isolated following biotinylation and identified by tandem mass spectrometry. The corresponding non-prime side sequences were derived from human proteome databases using bioinformatics. Sequencing of 2,405 individual cleaved peptides allowed for the development of the family consensus protease cleavage site specificity revealing a strong specificity for arginine in the P1 position and surprisingly a lysine in P1′ position. TTSP cleavage between R↓K was confirmed using synthetic peptides. By parsing through known substrates and known structures of TTSP catalytic domains, and by modeling the remainder, structural explanations for this strong specificity were derived. Conclusions Degradomics analysis of 2,405 cleavage sites revealed a similar and characteristic TTSP family specificity at the P1 and P1′ positions for arginine and lysine in unfolded peptides. The prime side is important for cleavage specificity, thus making these proteases unusual within the tryptic-enzyme class that generally has overriding non-prime side specificity.
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Affiliation(s)
- Olivier Barré
- Centre for Blood Research, Department of Oral Biological & Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Antoine Dufour
- Centre for Blood Research, Department of Oral Biological & Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological & Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Department of Oral Biological & Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - François Béliveau
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Richard Leduc
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christopher M. Overall
- Centre for Blood Research, Department of Oral Biological & Medical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- * E-mail:
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18
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Jin HB, Kang Y, Zhang J, Wu T, Wang Q. Interaction between tissue-type plasminogen activator and ligands grafted onto hydrogel. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.749408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Abstract
Hepsin is a type II transmembrane serine protease that is expressed in several human tissues. Overexpression of hepsin has been found to correlate with tumour progression and metastasis, which is so far best studied for prostate cancer, where more than 90% of such tumours show this characteristic. To enable improved future patient treatment, we have developed a monoclonal humanized antibody that selectively inhibits human hepsin and does not inhibit other related proteases. We found that our antibody, hH35, potently inhibits hepsin enzymatic activity at nanomolar concentrations. Kinetic characterization revealed non-linear, slow, tight-binding inhibition. This correlates with the crystal structure we obtained for the human hepsin-hH35 antibody Fab fragment complex, which showed that the antibody binds hepsin around α3-helix, located far from the active centre. The unique allosteric mode of inhibition of hH35 is distinct from the recently described HGFA (hepatocyte growth factor activator) allosteric antibody inhibition. We further explain how a small change in the antibody design induces dramatic structural rearrangements in the hepsin antigen upon binding, leading to complete enzyme inactivation.
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20
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García-Sosa AT, Mancera RL. Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex. Mol Inform 2010; 29:589-600. [PMID: 27463454 DOI: 10.1002/minf.201000007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 07/29/2010] [Indexed: 11/06/2022]
Abstract
The accurate calculation of the free energy of interaction of protein-water-ligand systems has an important role in molecular recognition and drug design that is often not fully considered. We report free energy thermodynamic integration calculations used to evaluate the effects of inclusion, neglect, and targeting and removal (i.e., systematic substitution by ligand functional groups) of an important, tightly bound, water molecule in the SH3 domain of Abl tyrosine kinase. The effects of this water molecule on the free energies of interaction of several Abl-SH3 domain-ligand systems reveal that there is an unfavourable free energy change associated with its removal into the bulk solvent. Only three substitutions by an additional functional group (out of methyl, ethyl, hydroxyl, amino, and amide groups) in the phenyl ring of a tyrosine in the peptide ligand resulted in a favourable change in the free energy of binding upon replacement of the ordered water molecule. This computational approach provides a direct route to the systematic and rigorous prediction of the thermodynamic influence of ordered, structural water molecules on ligand modification and optimization in drug design by calculating free energy changes in protein-water-ligand systems.
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Affiliation(s)
- Alfonso T García-Sosa
- Institute of Chemistry, University of Tartu, Jakobi 2-319, Tartu 51014, Estonia tel: + 372 737 5270; fax: + 372 737 5264. ,
| | - Ricardo L Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University of Technology, GPO Box U1987, Perth WA 6865, Australia
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21
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The cutting edge: membrane-anchored serine protease activities in the pericellular microenvironment. Biochem J 2010; 428:325-46. [PMID: 20507279 DOI: 10.1042/bj20100046] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The serine proteases of the trypsin-like (S1) family play critical roles in many key biological processes including digestion, blood coagulation, and immunity. Members of this family contain N- or C-terminal domains that serve to tether the serine protease catalytic domain directly to the plasma membrane. These membrane-anchored serine proteases are proving to be key components of the cell machinery for activation of precursor molecules in the pericellular microenvironment, playing vital functions in the maintenance of homoeostasis. Substrates activated by membrane-anchored serine proteases include peptide hormones, growth and differentiation factors, receptors, enzymes, adhesion molecules and viral coat proteins. In addition, new insights into our understanding of the physiological functions of these proteases and their involvement in human pathology have come from animal models and patient studies. The present review discusses emerging evidence for the diversity of this fascinating group of membrane serine proteases as potent modifiers of the pericellular microenvironment through proteolytic processing of diverse substrates. We also discuss the functional consequences of the activities of these proteases on mammalian physiology and disease.
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22
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Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Bandyopadhyay D, Mehler EL. Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment. Proteins 2008; 72:646-59. [PMID: 18247345 DOI: 10.1002/prot.21958] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A general method has been developed to characterize the hydrophobicity or hydrophilicity of the microenvironment (MENV), in which a given amino acid side chain is immersed, by calculating a quantitative property descriptor (QPD) based on the relative (to water) hydrophobicity of the MENV. Values of the QPD were calculated for a test set of 733 proteins to analyze the modulating effects on amino acid residue properties by the MENV in which they are imbedded. The QPD values and solvent accessibility were used to derive a partitioning of residues based on the MENV hydrophobicities. From this partitioning, a new hydrophobicity scale was developed, entirely in the context of protein structure, where amino acid residues are immersed in one or more "MENVpockets." Thus, the partitioning is based on the residues "sampling" a large number of "solvents" (MENVs) that represent a very large range of hydrophobicity values. It was found that the hydrophobicity of around 80% of amino acid side chains and their MENV are complementary to each other, but for about 20%, the MENV and their imbedded residue can be considered as mismatched. Many of these mismatches could be rationalized in terms of the structural stability of the protein and/or the involvement of the imbedded residue in function. The analysis also indicated a remarkable conservation of local environments around highly conserved active site residues that have similar functions across protein families, but where members have relatively low sequence homology. Thus, quantitative evaluation of this QPD is suggested, here, as a tool for structure-function prediction, analysis, and parameter development for the calculation of properties in proteins.
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Affiliation(s)
- Debashree Bandyopadhyay
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA
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24
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Rational design of peptide ligand for affinity chromatography of tissue-type plasminogen activator by the combination of docking and molecular dynamics simulations. J Chromatogr A 2007; 1175:249-58. [DOI: 10.1016/j.chroma.2007.10.074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 10/22/2022]
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25
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Zesławska E, Stürzebecher J, Oleksyn BJ. Geometry of GPPE binding to picrate and to the urokinase type plasminogen activator. Bioorg Med Chem Lett 2007; 17:6212-5. [PMID: 17905583 DOI: 10.1016/j.bmcl.2007.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 08/31/2007] [Accepted: 09/05/2007] [Indexed: 10/22/2022]
Abstract
Crystal structure of 2-(4-guanidynephenyl)-1-phenyl-ethanone (GPPE) in two different environments was determined in order to compare the binding geometry of these compound to a simple picrate anion and to protein, urokinase-type plasminogen activator (uPA), which may be treated as a target for anti-cancer drugs. It was shown that the conformation and the hydrogen-bonding formation by GPPE molecule are similar in both environments, but several important differences were discovered and described.
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Affiliation(s)
- Ewa Zesławska
- Department of Chemistry, Pedagogical University, ul. Podchorazych 2, 30-084 Kraków, Poland
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26
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Zhu M, Gokhale VM, Szabo L, Munoz RM, Baek H, Bashyam S, Hurley LH, Von Hoff DD, Han H. Identification of a novel inhibitor of urokinase-type plasminogen activator. Mol Cancer Ther 2007; 6:1348-56. [PMID: 17431113 DOI: 10.1158/1535-7163.mct-06-0520] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Urokinase-type plasminogen activator (uPA), a highly restricted serine protease, plays an important role in the regulation of diverse physiologic and pathologic processes. Strong clinical and experimental evidence has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients. uPA has been considered as a promising molecular target for development of anticancer drugs. Here, we report the identification of several new uPA inhibitors using a high-throughput screen from a chemical library. From these uPA inhibitors, molecular modeling and docking studies identified 4-oxazolidinone as a novel lead pharmacophore. Optimization of the 4-oxazolidinone pharmacophore resulted in a series of structurally modified compounds with improved potency and selectivity. One of the 4-oxazolidinone analogues, UK122, showed the highest inhibition of uPA activity. The IC(50) of UK122 in a cell-free indirect uPA assay is 0.2 micromol/L. This compound also showed no or little inhibition of other serine proteases such as thrombin, trypsin, plasmin, and the tissue-type plasminogen activator, indicating its high specificity against uPA. Moreover, UK122 showed little cytotoxicity against CFPAC-1 cells (IC(50) >100 micromol/L) but significantly inhibited the migration and invasion of this pancreatic cancer cell line. Our data show that UK122 could potentially be developed as a new anticancer agent that prevents the invasion and metastasis of pancreatic cancer.
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Affiliation(s)
- Ming Zhu
- Division of Clinical Translational Research, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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27
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Hansen M, Wind T, Blouse GE, Christensen A, Petersen HH, Kjelgaard S, Mathiasen L, Holtet TL, Andreasen PA. A Urokinase-type Plasminogen Activator-inhibiting Cyclic Peptide with an Unusual P2 Residue and an Extended Protease Binding Surface Demonstrates New Modalities for Enzyme Inhibition. J Biol Chem 2005; 280:38424-37. [PMID: 16141208 DOI: 10.1074/jbc.m505933200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To find new principles for inhibiting serine proteases, we screened phage-displayed random peptide repertoires with urokinase-type plasminogen activator (uPA) as the target. The most frequent of the isolated phage clones contained the disulfide bridge-constrained sequence CSWRGLENHRMC, which we designated upain-1. When expressed recombinantly with a protein fusion partner, upain-1 inhibited the enzymatic activity of uPA competitively with a temperature and pH-dependent K(i), which at 25 degrees C and pH 7.4 was approximately 500 nm. At the same conditions, the equilibrium dissociation constant K(D), monitored by displacement of p-aminobenzamidine from the specificity pocket of uPA, was approximately 400 nm. By an inhibitory screen against other serine proteases, including trypsin, upain-1 was found to be highly selective for uPA. The cyclical structure of upain-1 was indispensable for uPA binding. Alanine-scanning mutagenesis identified Arg(4) of upain-1 as the P(1) residue and indicated an extended binding interaction including the specificity pocket and the 37-, 60-, and 97-loops of uPA and the P(1), P(2), P(3)', P(4)', and the P(5)' residues of upain-1. Substitution with alanine of the P(2) residue, Trp(3), converted upain-1 into a distinct, although poor, uPA substrate. Upain-1 represents a new type of uPA inhibitor that achieves selectivity by targeting uPA-specific surface loops. Most likely, the inhibitory activity depends on its cyclical structure and the unusual P(2) residue preventing the scissile bond from assuming a tetrahedral geometry and thus from undergoing hydrolysis. Peptide-derived inhibitors such as upain-1 may provide novel mechanistic information about enzyme-inhibitor interactions and alternative methodologies for designing effective protease inhibitors.
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Affiliation(s)
- Martin Hansen
- Department of Molecular Biology, University of Aarhus, Gustav Wied's Vej 10C, 8000 Aarhus C, Denmark
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28
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Tang J, Yu CL, Williams SR, Springman E, Jeffery D, Sprengeler PA, Estevez A, Sampang J, Shrader W, Spencer J, Young W, McGrath M, Katz BA. Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. J Biol Chem 2005; 280:41077-89. [PMID: 16199530 DOI: 10.1074/jbc.m506766200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.
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Affiliation(s)
- Jie Tang
- Department of Structural Chemistry, Celera Genomics, South San Francisco, California 94080, USA
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29
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Jensen CM, Lindsay KB, Andreasen P, Skrydstrup T. Synthesis of a Hydroxyethylene Isostere of the Tripeptide Arg-Gly-Leu via a Convergent Acyl-like Radical Addition Strategy. J Org Chem 2005; 70:7512-9. [PMID: 16149778 DOI: 10.1021/jo0505775] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A hydroxyethylene isostere of the tripeptide Arg-Gly-Leu, representing an important fragment of a novel cyclic-peptide-based uPA inhibitor, was synthesized in few steps employing as the key step a samarium diiodide promoted coupling of either the 4-thiopyridyl ester of N(alpha)-Fmoc- or N(alpha)-Cbz-protected L-ornithine with the N-acryloyl derivative of L-leucine methyl ester. Epimerization under the coupling conditions at the chiral center in the alpha-position to the ketone was demonstrated not to take place. A stereoselective reduction of the Cbz-protected aminoketone obtained from this radical reaction was promoted by the same single-electron reducing agent in the presence of methanol providing the syn-amino alcohol with a diastereoselectivity of 85:15. With the use of lithium tri-tert-butoxyaluminum hydride in methanol, the corresponding anti-isomer was obtained almost exclusively. Subsequent elaboration of the ornithine moiety in the anti-isomer by introduction of the guanidine group followed by hydrolysis of the C-terminal ester bond and protection of the alcohol as its tert-butyldimethylsilyl ether provided the desired tripeptide mimic. The long reaction times required for the radical addition reactions with N(delta)-Boc-L-ornithine (up to 5 days) led to a short study where a series of 4-thiopyridyl esters of Cbz-protected amino acids were reacted with two acrylates. Whereas N(delta)-Boc-L-ornithine, alanine, phenylalanine, proline, and leucine all provided the aminoketone in 43-79% yield, valine only afforded traces of the coupling product.
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Affiliation(s)
- Christina M Jensen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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