1
|
Zhen S, Wang G, Li X, Yang J, Yu J, Wang Y. Discovering peptide inhibitors of thrombin as a strategy for anticoagulation. Medicine (Baltimore) 2024; 103:e36849. [PMID: 38215083 PMCID: PMC10783423 DOI: 10.1097/md.0000000000036849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
Unusual blood clots can cause serious health problems, such as lung embolism, stroke, and heart attack. Inhibiting thrombin activity was adopted as an effective strategy for preventing blood clots. In this study, we explored computational-based method for designing peptide inhibitors of human thrombin therapeutic peptides to prevent platelet aggregation. The random peptides and their 3-dimentional structures were generated to build a virtual peptide library. The generated peptides were docked into the binding pocket of human thrombin. The designed strong binding peptides were aligned with the native binder by comparative study, and we showed the top 5 peptide binders display strong binding affinity against human thrombin. The 5 peptides were synthesized and validated their inhibitory activity. Our result showed the 5-mer peptide AEGYA, EVVNQ, and FASRW with inhibitory activity against thrombin, range from 0.53 to 4.35 μM. In vitro anti-platelet aggregation assay was carried out, suggesting the 3 peptides can inhibit the platelet aggregation induced by thrombin. This study showed computer-aided peptide inhibitor design can be a robust method for finding potential binders for thrombin, which provided solutions for anticoagulation.
Collapse
Affiliation(s)
- Shuxin Zhen
- Department of Internal Medicine, Tangshan Gongren Hospital, Tangshan, Hebei, China
| | - Guiping Wang
- Department of Cardiology, Tangshan Gongren Hospital, Tangshan, Hebei, China
| | - Xiaoli Li
- Department of General Practice, Tangshan Gongren Hospital, Tangshan, Hebei, China
| | - Jing Yang
- Department of Cardiology, Tangshan Gongren Hospital, Tangshan, Hebei, China
| | - Jiaxin Yu
- Department of Cardiology, Tangshan Gongren Hospital, Tangshan, Hebei, China
| | - Yucong Wang
- Department of Visual Communication Design, Gengdan Institute of Beijing University of Technology, Beijing, China
| |
Collapse
|
2
|
Identification and in silico analysis of antithrombotic peptides from the enzymatic hydrolysates of Tenebrio molitor larvae. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-019-03381-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
3
|
Qiao M, Tu M, Chen H, Mao F, Yu C, Du M. Identification and In Silico Prediction of Anticoagulant Peptides from the Enzymatic Hydrolysates of Mytilus edulis Proteins. Int J Mol Sci 2018; 19:ijms19072100. [PMID: 30029529 PMCID: PMC6073223 DOI: 10.3390/ijms19072100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/13/2023] Open
Abstract
Mytilus edulis is a typical marine bivalve mollusk. Many kinds of bioactive components with nutritional and pharmaceutical activities in Mytilus edulis were reported. In this study, eight different parts of Mytilus edulis tissues, i.e., the foot, byssus, pedal retractor muscle, mantle, gill, adductor muscle, viscera, and other parts, were separated and the proteins from these tissues were prepared. A total of 277 unique peptides from the hydrolysates of different proteins were identified by UPLC-Q-TOF-MS/MS, and the molecular weight distribution of the peptides in different tissues was investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The bioactivity of the peptides was predicted through the Peptide Ranker database and molecular docking. Moreover, the peptides from the adductor muscle were chosen to do the active validation of anticoagulant activity. The active mechanism of three peptides from the adductor muscle, VQQELEDAEERADSAEGSLQK, RMEADIAAMQSDLDDALNGQR, and AAFLLGVNSNDLLK, were analyzed by Discovery Studio 2017, which also explained the anticoagulant activity of the hydrolysates of proteins from adductor muscle. This study optimized a screening and identification method of bioactive peptides from enzymatic hydrolysates of different tissues in Mytilus edulis.
Collapse
Affiliation(s)
- Meiling Qiao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Maolin Tu
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Hui Chen
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Fengjiao Mao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Cuiping Yu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Ming Du
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| |
Collapse
|
4
|
Qiao M, Tu M, Wang Z, Mao F, Chen H, Qin L, Du M. Identification and Antithrombotic Activity of Peptides from Blue Mussel (Mytilus edulis) Protein. Int J Mol Sci 2018; 19:E138. [PMID: 29300301 PMCID: PMC5796087 DOI: 10.3390/ijms19010138] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
The blue mussel (Mytilus edulis) reportedly contains many bioactive components of nutritional value. Water-, salt- and acid-soluble M. edulis protein fractions were obtained and the proteins were trypsinized. The resultant peptides were analyzed by ultra-performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS). 387 unique peptides were identified that matched 81 precursor proteins. Molecular mass distributions of the proteins and peptides were analyzed by sodium dodecyl sulfate-polyacryl amide gel electrophoresis (SDS-PAGE). The differences between the three protein samples were studied by Venn diagram of peptide and protein compositions. Toxicity, allergic and antithrombotic activity of peptides was predicted using database website and molecular docking respectively. The antithrombotic activity of enzymatic hydrolysate from water-, salt- and acid-soluble M. edulis protein were 40.17%, 85.74%, 82.00% at 5 mg/mL, respectively. Active mechanism of antithrombotic peptide (ELEDSLDSER) was also research about amino acid binding sites and interaction, simultaneously.
Collapse
Affiliation(s)
- Meiling Qiao
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Maolin Tu
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhenyu Wang
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Fengjiao Mao
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Hui Chen
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Lei Qin
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Ming Du
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| |
Collapse
|
5
|
Thrombin inhibitory peptides derived from Mytilus edulis proteins: identification, molecular docking and in silico prediction of toxicity. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2946-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
6
|
Tu M, Feng L, Wang Z, Qiao M, Shahidi F, Lu W, Du M. Sequence analysis and molecular docking of antithrombotic peptides from casein hydrolysate by trypsin digestion. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.03.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
7
|
A Peptide Microarray-Based Fluorescent and Resonance Light Scattering Assay for Screening Thrombin Inhibitor. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60802-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
8
|
Sapi J, Schmidt F, Van Hijfte L, George P. Interfacing chemical biology and drug discovery: report from the 50th International Conference on Medicinal Chemistry of the SCT (French Medicinal Chemistry Society), July 2-4, 2014, Rouen, France. ACS Chem Biol 2014; 9:2702-7. [PMID: 25476010 DOI: 10.1021/cb5009469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janos Sapi
- SCT Vice-President, UMR CNRS 7312, Université de Reims-Champagne-Ardenne, 51 rue Cognacq-Jay, F-51069 Reims Cedex, France
| | - Frédéric Schmidt
- SCT Communication Officer, Institut Curie, Research Center, CNRS UMR3666, INSERM U1143, 26 rue d’Ulm, F-75248 Paris, France
| | - Luc Van Hijfte
- NovAliX, BioParc, 850 Blvd Sébastien Brant, BP 30170, F-67405 Illkirch Cedex, France
| | - Pascal George
- SCT President,
Independent Scientific Expert and Adviser, F-78730 Longvilliers, France
| |
Collapse
|
9
|
Young RJ. The successful quest for oral factor Xa inhibitors; learnings for all of medicinal chemistry? Bioorg Med Chem Lett 2011; 21:6228-35. [DOI: 10.1016/j.bmcl.2011.08.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/26/2011] [Accepted: 08/27/2011] [Indexed: 11/29/2022]
|
10
|
Arnold M, Bittermann H, Kalbfuss-Zimmermann B, Neumann T, Schmidt K, Sekul R, Hilbrig F, Ludolph H, Freitag R. Antibody purification by affinity chromatography based on small molecule affinity ligands identified by SPR-based screening of chemical microarrays. J Chromatogr A 2011; 1218:4649-59. [DOI: 10.1016/j.chroma.2011.05.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 05/09/2011] [Accepted: 05/10/2011] [Indexed: 11/28/2022]
|
11
|
Cole JC, Korb O, Olsson TSG, Liebeschuetz J. The Basis for Target-Based Virtual Screening: Protein Structures. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/9783527633326.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
|
12
|
Wang G, Goyal N, Hopkinson B. Preparation of l-proline based aeruginosin 298-A analogs: Optimization of the P1-moiety. Bioorg Med Chem Lett 2009; 19:3798-803. [DOI: 10.1016/j.bmcl.2009.04.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
|
13
|
Geschwindner S, Olsson LL, Albert JS, Deinum J, Edwards PD, de Beer T, Folmer RHA. Discovery of a novel warhead against beta-secretase through fragment-based lead generation. J Med Chem 2007; 50:5903-11. [PMID: 17985861 DOI: 10.1021/jm070825k] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragment-based lead generation was applied to find novel small-molecule inhibitors of beta-secretase (BACE-1), a key target for the treatment of Alzheimer's disease. Fragment hits coming from a 1D NMR screen were characterized by BIAcore, and the most promising compounds were soaked into protein crystals to help the rational design of more potent hit analogues. Problems arising due to our inability to grow BACE-1 crystals at the biologically relevant pH at which the screen was run were overcome by using endothiapepsin as a surrogate aspartyl protease. Among others, we identified 6-substituted isocytosines as a novel warhead against BACE-1, and the accompanying paper in this journal describes how these were optimized to a lead series of nanomolar inhibitors.1.
Collapse
|
14
|
Congreve M, Murray CW, Carr R, Rees DC. Chapter 28 Fragment-Based Lead Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY VOLUME 42 2007. [DOI: 10.1016/s0065-7743(07)42028-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
15
|
Maier S, Frank M, Rau H, Lewandrowski P, Uhrig R, Keil O, Deppe H, Müller N, Vanier C, Mannsperger H, Zepter S, Junker HD. Synthesis and Quality Control of Thiol Tagged Compound Libraries for Chemical Microarrays. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200640125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|