1
|
Kim JH, Lee CJ, Yu YS, Aryal YP, Kim S, Suh JY, Kim JY, Min SH, Cha IT, Lee HY, Shin SY, Cho SJ. Transcriptomic profiling and the first spatial expression analysis of candidate genes in the salivary gland of the East Asian medicinal leech, Hirudo nipponia. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105125. [PMID: 38158145 DOI: 10.1016/j.dci.2023.105125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Hirudo nipponia, a blood-sucking leech native to East Asia, possesses a rich repertoire of active ingredients in its saliva, showcasing significant medical potential due to its anticoagulant, anti-inflammatory, and antibacterial effects against human diseases. Despite previous studies on the transcriptomic and proteomic characteristics of leech saliva, which have identified medicinal compounds, our knowledge of tissue-specific transcriptomes and their spatial expression patterns remains incomplete. In this study, we conducted an extensive transcriptomic profiling of the salivary gland tissue in H. nipponia based on de novo assemblies of tissue-specific transcriptomes from the salivary gland, teeth, and general head region. Through gene ontology (GO) analysis and hierarchical clustering, we discovered a novel set of anti-coagulant factors-i.e., Hni-Antistasin, Hni-Ghilanten, Hni-Bdellin, Hni-Hirudin-as well as a previously unrecognized immune-related gene, Hni-GLIPR1 and uncharacterized salivary gland specific transcripts. By employing in situ hybridization, we provided the first visualization of gene expression sites within the salivary gland of H. nipponia. Our findings expand on our understanding of transcripts specifically expressed in the salivary gland of blood-sucking leeches, offering valuable resources for the exploration of previously unidentified substances with medicinal applications.
Collapse
Affiliation(s)
- Jung-Hyeuk Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea; Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention, Incheon, 22689, Republic of Korea
| | - Chan-Jun Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yun-Sang Yu
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yam Prasad Aryal
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sangil Kim
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jo-Young Suh
- Department of Periodontology, School of Dentistry, IHBR Kyungpook National University, Daegu, 41940, Republic of Korea
| | - Jae-Young Kim
- Department of Biochemistry, School of Dentistry, IHBR, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Sun Hong Min
- Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - In-Tae Cha
- Species Diversity Research Division, National Institute of Biological Resources(NIBR), Incheon, 22689, Republic of Korea
| | - Hae-Youn Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
| | - Song Yub Shin
- Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
| |
Collapse
|
2
|
Goettig P, Chen X, Harris JM. Correlation of Experimental and Calculated Inhibition Constants of Protease Inhibitor Complexes. Int J Mol Sci 2024; 25:2429. [PMID: 38397107 PMCID: PMC10889394 DOI: 10.3390/ijms25042429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Predicting the potency of inhibitors is key to in silico screening of promising synthetic or natural compounds. Here we describe a predictive workflow that provides calculated inhibitory values, which concord well with empirical data. Calculations of the free interaction energy ΔG with the YASARA plugin FoldX were used to derive inhibition constants Ki from PDB coordinates of protease-inhibitor complexes. At the same time, corresponding KD values were obtained from the PRODIGY server. These results correlated well with the experimental values, particularly for serine proteases. In addition, analyses were performed for inhibitory complexes of cysteine and aspartic proteases, as well as of metalloproteases, whereby the PRODIGY data appeared to be more consistent. Based on our analyses, we calculated theoretical Ki values for trypsin with sunflower trypsin inhibitor (SFTI-1) variants, which yielded the more rigid Pro14 variant, with probably higher potency than the wild-type inhibitor. Moreover, a hirudin variant with an Arg1 and Trp3 is a promising basis for novel thrombin inhibitors with high potency. Further examples from antibody interaction and a cancer-related effector-receptor system demonstrate that our approach is applicable to protein interaction studies beyond the protease field.
Collapse
Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Xingchen Chen
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| |
Collapse
|
3
|
Acquasaliente L, Pierangelini A, Pagotto A, Pozzi N, De Filippis V. From haemadin to haemanorm: Synthesis and characterization of full-length haemadin from the leech Haemadipsa sylvestris and of a novel bivalent, highly potent thrombin inhibitor (haemanorm). Protein Sci 2023; 32:e4825. [PMID: 37924304 PMCID: PMC10683372 DOI: 10.1002/pro.4825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Hirudin from Hirudo medicinalis is a bivalent α-Thrombin (αT) inhibitor, targeting the enzyme active site and exosite-I, and is currently used in anticoagulant therapy along with its simplified analogue hirulog. Haemadin, a small protein (57 amino acids) isolated from the land-living leech Haemadipsa sylvestris, selectively inhibits αT with a potency identical to that of recombinant hirudin (KI = 0.2 pM), with which it shares a common disulfide topology and overall fold. At variance with hirudin, haemadin targets exosite-II and therefore (besides the free protease) it also blocks thrombomodulin-bound αT without inhibiting the active intermediate meizothrombin, thus offering potential advantages over hirudin. Here, we produced in reasonably high yields and pharmaceutical purity (>98%) wild-type haemadin and the oxidation resistant Met5 → nor-Leucine analogue, both inhibiting αT with a KI of 0.2 pM. Thereafter, we used site-directed mutagenesis, spectroscopic, ligand-displacement, and Hydrogen/Deuterium Exchange-Mass Spectrometry techniques to map the αT regions relevant for the interaction with full-length haemadin and with the synthetic N- and C-terminal peptides Haem(1-10) and Haem(45-57). Haem(1-10) competitively binds to/inhibits αT active site (KI = 1.9 μM) and its potency was enhanced by 10-fold after Phe3 → β-Naphthylalanine exchange. Conversely to full-length haemadin, haem(45-57) displays intrinsic affinity for exosite-I (KD = 1.6 μM). Hence, we synthesized a peptide in which the sequences 1-9 and 45-57 were joined together through a 3-Glycine spacer to yield haemanorm, a highly potent (KI = 0.8 nM) inhibitor targeting αT active site and exosite-I. Haemanorm can be regarded as a novel class of hirulog-like αT inhibitors with potential pharmacological applications.
Collapse
Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Anna Pagotto
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Nicola Pozzi
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research CenterSaint Louis UniversitySt. LouisMissouriUSA
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| |
Collapse
|
4
|
Shi P, Wei J, You H, Chen S, Tan F, Lu Z. Cloning, characterization, and heterologous expression of a candidate Hirudin gene from the salivary gland transcriptome of Hirudo nipponia. Sci Rep 2023; 13:4943. [PMID: 36973525 PMCID: PMC10042815 DOI: 10.1038/s41598-023-32303-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
AbstractHirudin is a pharmacologically active substance in leeches with potent blood anticoagulation properties. Although recombinant hirudin production isolated from Hirudo medicinalis Linnaeus and Hirudinaria manillensis Lesson is known, to our knowledge, this study is the first to report recombinant hirudin expression and production from Hirudo nipponia Whitman. Thus, the present study aimed to clone and characterize the full-length cDNA of a candidate hirudin gene (c16237_g1), which is localized on the salivary gland transcriptome of H. nipponia, and further evaluate its recombinant production using a eukaryotic expression system. The 489-bp cDNA possessed several properties of the hirudin “core” motifs associated with binding to the thrombin catalytic pocket. A fusion expression vector (pPIC9K-hirudin) was constructed and successfully transformed into Pichia pastoris strain GS115 via electroporation. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis and western blot analysis confirmed hirudin expression. The recombinant protein was expressed with a yield of 6.68 mg/L culture. Mass spectrometry analysis further confirmed target protein expression. The concentration and antithrombin activity of purified hirudin were 1.67 mg/mL and 14,000 ATU/mL, respectively. These findings provide a basis for further elucidating the molecular anticoagulation mechanism of hirudin, and address China’s growing market demand for engineered H. nipponia-derived hirudin and hirudin-based drugs.
Collapse
|
5
|
Guerra Y, Armijos‐Jaramillo V, Pons T, Tejera E, Berry C. Canonical or noncanonical? Structural plasticity of serine protease-binding loops in Kunitz-STI protease inhibitors. Protein Sci 2023; 32:e4570. [PMID: 36660780 PMCID: PMC9885459 DOI: 10.1002/pro.4570] [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: 09/05/2022] [Revised: 12/08/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The Kunitz-Soybean Trypsin Inhibitor (Kunitz-STI) family is a large family of proteins with most of its members being protease inhibitors. The versatility of the inhibitory profile and the structural plasticity of these proteins, make this family a promising scaffold for designing new multifunctional proteins. Historically, Kunitz-STI inhibitors have been classified as canonical serine protease inhibitors, but new inhibitors with novel inhibition mechanisms have been described in recent years. Different inhibition mechanisms could be the result of different evolutionary pathways. In the present work, we performed a structural analysis of all the crystallographic structures available for Kunitz-STI inhibitors to characterize serine protease-binding loop structural features and locations. Our study suggests a relationship between the conformation of serine protease-binding loops and the inhibition mechanism, their location in the β-trefoil fold, and the plant source of the inhibitors. The classical canonical inhibitors of this family are restricted to plants from the Fabales order and bind their targets via the β4-β5 loop, whereas serine protease-binding loops in inhibitors from other plants lie mainly in the β5-β6 and β9-β10 loops. In addition, we found that the β5-β6 loop is used to inhibit two different families of serine proteases through a steric blockade inhibition mechanism. This work will help to change the general perception that all Kunitz-STI inhibitors are canonical inhibitors and proteins with protease-binding loops adopting noncanonical conformations are exceptions. Additionally, our results will help in the identification of protease-binding loops in uncharacterized or newly discovered inhibitors, and in the design of multifunctional proteins.
Collapse
Affiliation(s)
- Yasel Guerra
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Vinicio Armijos‐Jaramillo
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Tirso Pons
- Department of Immunology and OncologyNational Centre for Biotechnology (CNB‐CSIC)MadridSpain
| | - Eduardo Tejera
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Colin Berry
- Cardiff School of BiosciencesCardiff UniversityCardiffUK
| |
Collapse
|
6
|
Mo Z, Xiao Z, He C. Functional expression of a thrombin exosite I inhibitor triabin in Escherichia coli and elucidation of the role of key residues in its inhibitory activity. Biochimie 2022; 208:13-19. [PMID: 36580989 DOI: 10.1016/j.biochi.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Triabin, a lipocalin-like thrombin inhibitor from the saliva of the blood-sucking triatomine bug Triatoma pallidipennis, exhibits effective inhibition comparable to hirudin despite binding exclusively at exosite I. Interestingly, it was reported that higher triabin doses would not inhibit thrombin completely, which makes it a promising antithrombotic candidate agent with a larger therapeutic window. However, few structural and functional studies about triabin have been reported in the past three decades, mostly due to the lack of a reliable and practicable recombinant expression technology for this seemingly small protein. In this work, we have adopted the SUMO fusion technology for the expression of triabin in E. coli cells-with facile refolding and purification procedures-and the bioactive triabin was produced in ∼12 mg/L culture medium. Subsequently, the structure-function studies through extensive site-directed mutagenesis reveal that triabin's Phe-106 involved in the hydrophobic contacts plays a surprisingly important role in the thrombin inhibition, in contrast to the negatively charged residues Asp-135 or Glu-128 involved in the salt-bridge interaction. As such, this study complements our understanding of the interaction mechanism of natural thrombin inhibitors, which should facilitate the development of anticoagulant drugs with a novel mode of action against thrombin.
Collapse
Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Zhenbang Xiao
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China.
| |
Collapse
|
7
|
Ma S, Fan W, Zhang J. Network pharmacology study on the potential effect mechanism of Chuanzhi Tongluo Capsule in the treatment of cerebral infarction. Medicine (Baltimore) 2022; 101:e30916. [PMID: 36254030 PMCID: PMC9575740 DOI: 10.1097/md.0000000000030916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Chuanxiong Tongluo capsules have been widely used to treat recovered stroke and cerebral infarction, but their specific therapeutic mechanism is not well understood. METHODS This study aims to investigate the mechanism of action for Chuanzhi Tongluo capsule on cerebral infarction based on a network pharmacology approach. The TCMSP platform collected the chemical composition of Chuanzhi Tongluo capsules. Its potential targets were predicted by Swiss target prediction and standardized using the Uniprot database for gene normalization. Meanwhile, the OMIM, Genecards, and TTD databases were used to obtain the targets related to cerebral infarction. The standard targets of Chuanzhi Tongluo capsule and cerebral infarction were uploaded to the STRING database to construct protein-protein interaction networks. Topological methods analyzed the key targets and components in the drug-component-disease-target network. Gene ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the shared targets were performed using the DAVID database. RESULTS A total of 105 active ingredients and 427 targets were associated with Chuanzhi Tongluo capsule, and there were 3055 targets related to cerebral infarction disease and 240 common targets between the two keywords. The key targets included INS, ALB, IL-6, VEGFA, TNF, and TP53. The conduction pathways involved include the calcium signaling pathway, cAMP signaling pathway, cGMP-PKG signaling pathway, and TNF signaling pathway. CONCLUSION The active ingredients in Chuanzhi Tongluo capsule may participate in the therapeutic process of cerebral infarction by regulating the calcium, cAMP, cGMP-PKG, and TNF signaling pathway through critical targets such as INS, ALB, IL-6, VEGFA, TNF, and TP53.
Collapse
Affiliation(s)
- Shan Ma
- Department of Traditional Chinese Medicine, the Second Hospital of Shandong University, Jinan, China
| | - Wenhui Fan
- Department of Traditional Chinese Medicine, the Second Hospital of Shandong University, Jinan, China
| | - Jianxin Zhang
- Department of Traditional Chinese Medicine, the Second Hospital of Shandong University, Jinan, China
- *Correspondence: Jianxin Zhang, Department of Traditional Chinese Medicine, the Second Hospital of Shandong University, No.247, Beiyuan Road, Tianqiao District, Jinan, Shandong 250014, China (e-mail: )
| |
Collapse
|
8
|
Yang Y, Liang M, Wang R, He C. Chemical protein synthesis elucidates key modulation mechanism of the tyrosine-O-sulfation in inducing strengthened inhibitory activity of hirudin. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
9
|
Reddy KA, Sahoo DK, Moi S, Gowd KH. Conformational change due to replacement of disulfide with selenosulfide and diselenide in dipeptide vicinal cysteine loop. Comput Biol Chem 2022; 97:107635. [DOI: 10.1016/j.compbiolchem.2022.107635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/21/2021] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
|
10
|
Sun Y, Wang B, Pei J, Luo Y, Yuan N, Xiao Z, Wu H, Luo C, Wang J, Wei S, Pei Y, Fu S, Wang D. Molecular dynamic and pharmacological studies on protein-engineered hirudin variants of Hirudinaria manillensis and Hirudo medicinalis. Br J Pharmacol 2022; 179:3740-3753. [PMID: 35135035 DOI: 10.1111/bph.15816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND AND PURPOSE Hirudin variants are the most powerful thrombin inhibitors discovered to date, with a lower risk of bleeding than heparin. For anticoagulation, the C-termini of hirudins bind to the exocite I of thrombin. Anticoagulant effects of gene-recombinant hirudin are weaker than natural hirudin for the reason of lacking tyrosine-O-sulfation at C terminus. EXPERIMENTAL APPROACH The integrative pharmacological study applied molecular dynamic, molecular biological, and in vivo and in vitro experiments to elucidate the anticoagulant effects of protein-engineered hirudins. KEY RESULTS Molecular dynamic (MD) analysis showed that modifications of the C-termini of hirudin variant 1 of Hirudo medicinalis (HV1) and hirudin variant 2 of Hirudinaria manillensis (HM2) changed the binding energy of the C-termini to human thrombin. The study indicated Asp61 of HM2 that corresponds to sulfated Tyr63 of HV1 is critical for inhibiting thrombin activities, and the anticoagulant effects of HV1 and HM2 were improved when the amino acid residues adjacent to Asp61 were mutated to Asp, such as the prolongation of the activated partial thromboplastin time (APTT), prothrombin time (PT) and thrombin time (TT) of human blood, and decreased Ki and IC50 values. In the in vivo experiments, mutations at C-termini of HV1 and HM2 significantly changed APTT, PT and TT. CONCLUSION AND IMPLICATIONS The study indicated that the anticoagulant effects of gene-engineered HM2 are stronger than gene-engineered HV1, and HM2-E60D-I62D has the strongest effects and could be an antithrombotic medicine with better therapeutic effects.
Collapse
Affiliation(s)
- Yan Sun
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Baochun Wang
- The First Department of Gastrointestinal Surgery, Hainan General Hospital, Haikou, Hainan, China
| | - Jinli Pei
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China.,Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ying Luo
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Nan Yuan
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Hao Wu
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China.,Central Laboratory, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Chenghui Luo
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Jiaxuan Wang
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Shuangshuang Wei
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Yechun Pei
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Shengmiao Fu
- Department of Medical Laboratory Science, Hainan General Hospital, Haikou, Hainan, China
| | - Dayong Wang
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China.,Key laboratory of Tropical Biological Resources of the Ministry of Education of China, Hainan University, Haikou, Hainan, China
| |
Collapse
|
11
|
Mollnes TE, Storm BS, Brekke OL, Nilsson PH, Lambris JD. Application of the C3 inhibitor compstatin in a human whole blood model designed for complement research - 20 years of experience and future perspectives. Semin Immunol 2022; 59:101604. [PMID: 35570131 DOI: 10.1016/j.smim.2022.101604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/23/2022] [Indexed: 01/15/2023]
Abstract
The complex molecular and cellular biological systems that maintain host homeostasis undergo continuous crosstalk. Complement, a component of innate immunity, is one such system. Initially regarded as a system to protect the host from infection, complement has more recently been shown to have numerous other functions, including involvement in embryonic development, tissue modeling, and repair. Furthermore, the complement system plays a major role in the pathophysiology of many diseases. Through interactions with other plasma cascades, including hemostasis, complement activation leads to the broad host-protective response known as thromboinflammation. Most complement research has been limited to reductionistic models of purified components and cells and their interactions in vitro. However, to study the pathophysiology of complement-driven diseases, including the interaction between the complement system and other inflammatory systems, holistic models demonstrating only minimal interference with complement activity are needed. Here we describe two such models; whole blood anticoagulated with either the thrombin inhibitor lepirudin or the fibrin polymerization peptide blocker GPRP, both of which retain complement activity and preserve the ability of complement to be mutually reactive with other inflammatory systems. For instance, to examine the relative roles of C3 and C5 in complement activation, it is possible to compare the effects of the C3 inhibitor compstatin effects to those of inhibitors of C5 and C5aR1. We also discuss how complement is activated by both pathogen-associated molecular patterns, inducing infectious inflammation caused by organisms such as Gram-negative and Gram-positive bacteria, and by sterile damage-associated molecular patterns, including cholesterol crystals and artificial materials used in clinical medicine. When C3 is inhibited, it is important to determine the mechanism by which inflammation is attenuated, i.e., whether the attenuation derives directly from C3 activation products or via downstream activation of C5, since the mechanism involved may determine the appropriate choice of inhibitor under various conditions. With some exceptions, most inflammatory responses are dependent on C5 and C5aR1; one exception is venous air embolism, in which air bubbles enter the blood circulation and trigger a mainly C3-dependent thromboembolism, with the formation of an active C3 convertase, without a corresponding C5 activation. Under such conditions, an inhibitor of C3 is needed to attenuate the inflammation. Our holistic blood models will be useful for further studies of the inhibition of any complement target, not just C3 or C5. The focus here will be on targeting the critical complement component, activation product, or receptor that is important for the pathophysiology in a variety of disease conditions.
Collapse
Affiliation(s)
- Tom E Mollnes
- Research Laboratory, Nordland Hospital, Bodø, Norway; Department of Immunology, Oslo University Hospital and University of Oslo, Norway; Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Benjamin S Storm
- Research Laboratory, Nordland Hospital, Bodø, Norway; Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Faculty of Nursing and Health Sciences, Nord University, Bodø, Norway
| | - Ole L Brekke
- Research Laboratory, Nordland Hospital, Bodø, Norway; Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway
| | - Per H Nilsson
- Department of Immunology, Oslo University Hospital and University of Oslo, Norway; Linnaeus Centre for Biomaterials Chemistry, Linnaeus University, 39182 Kalmar, Sweden; Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
12
|
Pelc LA, Koester SK, Kukla CR, Chen Z, Di Cera E. The active site region plays a critical role in Na + binding to thrombin. J Biol Chem 2022; 298:101458. [PMID: 34861239 PMCID: PMC8695361 DOI: 10.1016/j.jbc.2021.101458] [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: 10/05/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The catalytic activity of thrombin and other enzymes of the blood coagulation and complement cascades is enhanced significantly by binding of Na+ to a site >15 Å away from the catalytic residue S195, buried within the 180 and 220 loops that also contribute to the primary specificity of the enzyme. Rapid kinetics support a binding mechanism of conformational selection where the Na+-binding site is in equilibrium between open (N) and closed (N∗) forms and the cation binds selectively to the N form. Allosteric transduction of this binding step produces enhanced catalytic activity. Molecular details on how Na+ gains access to this site and communicates allosterically with the active site remain poorly defined. In this study, we show that the rate of the N∗→N transition is strongly correlated with the analogous E∗→E transition that governs the interaction of synthetic and physiologic substrates with the active site. This correlation supports the active site as the likely point of entry for Na+ to its binding site. Mutagenesis and structural data rule out an alternative path through the pore defined by the 180 and 220 loops. We suggest that the active site communicates allosterically with the Na+ site through a network of H-bonded water molecules that embeds the primary specificity pocket. Perturbation of the mobility of S195 and its H-bonding capabilities alters interaction with this network and influences the kinetics of Na+ binding and allosteric transduction. These findings have general mechanistic relevance for Na+-activated proteases and allosteric enzymes.
Collapse
Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Cassandra R Kukla
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
| |
Collapse
|
13
|
Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
Collapse
|
14
|
Müller C, Eickelmann C, Sponholz D, Hildebrandt JP. Short tail stories: the hirudin-like factors HLF6 and HLF7 of the Asian medicinal leech, Hirudinaria manillensis. Parasitol Res 2021; 120:3761-3769. [PMID: 34599360 PMCID: PMC8516769 DOI: 10.1007/s00436-021-07316-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/14/2021] [Indexed: 11/19/2022]
Abstract
The leech-derived hirudins and hirudin-like factors (HLFs) share a common molecule structure: a short N-terminus, a central globular domain, and an elongated C-terminal tail. All parts are important for function. HLF6 and HLF7 were identified in the Asian medicinal leech, Hirudinaria manillensis. The genes of both factors encode putative splice variants that differ in length and composition of their respective C-terminal tails. In either case, the tails are considerably shorter compared to hirudins. Here we describe the functional analyses of the natural splice variants and of synthetic variants that comprise an altered N-terminus and/or a modified central globular domain. All natural splice variants of HLF6 and HLF7 display no detectable thrombin-inhibitory potency. In contrast, some synthetic variants effectively inhibit thrombin, even with tails as short as six amino acid residues in length. Our data indicate that size and composition of the C-terminal tail of hirudins and HLFs can vary in a great extent, yet the full protein may still retain the ability to inhibit thrombin.
Collapse
Affiliation(s)
- Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany.
| | - Chantal Eickelmann
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany
| | - Dana Sponholz
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany
| |
Collapse
|
15
|
Kovach IM. Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System. Life (Basel) 2021; 11:396. [PMID: 33925363 PMCID: PMC8146069 DOI: 10.3390/life11050396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Inquiries into the participation of short hydrogen bonds in stabilizing transition states and intermediate states in the thrombin, factor Xa, plasmin and activated protein C-catalyzed reactions revealed that specific binding of effectors at Sn, n = 1-4 and S'n, n = 1-3 and at remote exosites elicit complex patterns of hydrogen bonding and involve water networks. The methods employed that yielded these discoveries include; (1) kinetics, especially partial or full kinetic deuterium solvent isotope effects with short cognate substrates and also with the natural substrates, (2) kinetic and structural probes, particularly low-field high-resolution nuclear magnetic resonance (1H NMR), of mechanism-based inhibitors and substrate-mimic peptide inhibitors. Short hydrogen bonds form at the transition states of the catalytic reactions at the active site of the enzymes as they do with mechanism-based covalent inhibitors of thrombin. The emergence of short hydrogen bonds at the binding interface of effectors and thrombin at remote exosites has recently gained recognition. Herein, I describe our contribution, a confirmation of this discovery, by low-field 1H NMR. The principal conclusion of this review is that proton sharing at distances below the sum of van der Waals radii of the hydrogen and both donor and acceptor atoms contribute to the remarkable catalytic prowess of serine proteases of the blood clotting system and other enzymes that employ acid-base catalysis. Proton bridges also play a role in tight binding in proteins and at exosites, i.e., allosteric sites, of enzymes.
Collapse
Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, DC 20064, USA
| |
Collapse
|
16
|
Study on the activity of recombinant mutant tissue-type plasminogen activator fused with the C-terminal fragment of hirudin. J Thromb Thrombolysis 2021; 52:880-888. [PMID: 33826053 DOI: 10.1007/s11239-021-02440-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/26/2021] [Indexed: 12/12/2022]
Abstract
In the present study, bifunctional fusion proteins were designed by fusing the kringle 2 and protease domains of tissue-type plasminogen activator (tPA) to the C-terminal fragment of hirudin. The thrombolytic and anticoagulant activities of these recombinant proteins from mammalian cells were investigated using in vitro coagulation models and chromogenic assays. The results showed that all assayed tPA mutants retained catalytic activity. The C-terminal fragment of hirudin may have weak affinity to thrombin and thus was insufficient to suppress thrombin-mediated fibrin agglutination. The strength of the thrombolytic activity only relied on the selected tPA sequences, and the fibrinolytic efficiency of single-chain protein significantly decreased. Our data indicate that truncated tPA combined with a hirudin peptide may provide a framework for the further development of a new antithrombotic agent.
Collapse
|
17
|
Diselenide crosslinks for enhanced and simplified oxidative protein folding. Commun Chem 2021; 4:30. [PMID: 36697775 PMCID: PMC9814483 DOI: 10.1038/s42004-021-00463-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/29/2021] [Indexed: 01/28/2023] Open
Abstract
The in vitro oxidative folding of proteins has been studied for over sixty years, providing critical insight into protein folding mechanisms. Hirudin, the most potent natural inhibitor of thrombin, is a 65-residue protein with three disulfide bonds, and is viewed as a folding model for a wide range of disulfide-rich proteins. Hirudin's folding pathway is notorious for its highly heterogeneous intermediates and scrambled isomers, limiting its folding rate and yield in vitro. Aiming to overcome these limitations, we undertake systematic investigation of diselenide bridges at native and non-native positions and investigate their effect on hirudin's folding, structure and activity. Our studies demonstrate that, regardless of the specific positions of these substitutions, the diselenide crosslinks enhanced the folding rate and yield of the corresponding hirudin analogues, while reducing the complexity and heterogeneity of the process. Moreover, crystal structure analysis confirms that the diselenide substitutions maintained the overall three-dimensional structure of the protein and left its function virtually unchanged. The choice of hirudin as a study model has implications beyond its specific folding mechanism, demonstrating the high potential of diselenide substitutions in the design, preparation and characterization of disulfide-rich proteins.
Collapse
|
18
|
Müller C, Lukas P, Sponholz D, Hildebrandt JP. The hirudin-like factors HLF3 and HLF4-hidden hirudins of European medicinal leeches. Parasitol Res 2020; 119:1767-1775. [PMID: 32363441 PMCID: PMC7261268 DOI: 10.1007/s00436-020-06697-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
The hirudin-like factors 3 (HLF3) and 4 (HLF4) belong to a new class of leech-derived factors and are present in specimens of the three European medicinal leeches, Hirudo medicinalis, Hirudo verbana, and Hirudo orientalis, respectively. Here we describe the functional analysis of natural and synthetic variants of HLF3 and HLF4. Whereas the natural variants display only very low or no detectable anti-coagulatory activities, modifications within the N-termini in combination with an exchange of the central globular domain have the potency to greatly enhance the inhibitory effects of respective HLF3 and HLF4 variants on blood coagulation. Our results support previous observations on the crucial importance of all parts (both the N- and C-termini as well as the central globular domains) of hirudin and HLF molecules for thrombin inhibition.
Collapse
Affiliation(s)
- Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany.
| | - Phil Lukas
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany
| | - Dana Sponholz
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, 17489, Greifswald, Germany
| |
Collapse
|
19
|
Zhou J, Li C, Chen A, Zhu J, Zou M, Liao H, Yu Y. Structural and functional relationship of Cassia obtusifolia trypsin inhibitor to understand its digestive resistance against Pieris rapae. Int J Biol Macromol 2020; 148:908-920. [PMID: 31981663 DOI: 10.1016/j.ijbiomac.2020.01.193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
Abstract
Although digestive resistance of Kunitz protease inhibitors has been reported extensively, the molecular mechanism is not well established. In the present study, the first X-ray structure of Cassia obtusifolia trypsin inhibitor (COTI), a member of Kunitz protease inhibitors, was solved at a resolution of 1.9 Å. The structure adopted a classic β-trefoil fold with the inhibitory loop protruding from the hydrophobic core. The role of Phe139, a unique residue in Kunitz protease inhibitors, and Arg63 in the COTI structure was verified by F139A and R63E mutants. COTI was a specific inhibitor of bovine trypsin and the result was also verified by COTI-trypsin complex formation. Meanwhile, COTI showed equivalent inhibitory activity with that of soybean trypsin inhibitor against bovine trypsin and midgut trypsin from Pieris rapae. The F139 and R63E mutants further indicated that inhibitory specificity and efficiency of COTI were closely related to the global framework, the conformation and the amino acid composition of reactive loop. Finally, a midgut trypsin from P. rapae (PrSP40), which might be involve in the food digestion, was proposed to be a potential target of COTI and might be a promising target for future crop-protection strategy. The results supported the digestive resistance of COTI.
Collapse
Affiliation(s)
- Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Chaolin Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China
| | - Anqi Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China
| | - Jianquan Zhu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China
| | - Meng Zou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Yamei Yu
- Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.
| |
Collapse
|
20
|
Müller C, Lukas P, Böhmert M, Hildebrandt J. Hirudin or hirudin‐like factor ‐ that is the question: insights from the analyses of natural and synthetic HLF variants. FEBS Lett 2019; 594:841-850. [DOI: 10.1002/1873-3468.13683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Christian Müller
- Animal Physiology and Biochemistry Zoological Institute and Museum University of Greifswald Germany
| | - Phil Lukas
- Animal Physiology and Biochemistry Zoological Institute and Museum University of Greifswald Germany
| | - Michel Böhmert
- Animal Physiology and Biochemistry Zoological Institute and Museum University of Greifswald Germany
| | - Jan‐Peter Hildebrandt
- Animal Physiology and Biochemistry Zoological Institute and Museum University of Greifswald Germany
| |
Collapse
|
21
|
Cheng B, Liu F, Guo Q, Lu Y, Shi H, Ding A, Xu C. Identification and characterization of hirudin-HN, a new thrombin inhibitor, from the salivary glands of Hirudo nipponia. PeerJ 2019; 7:e7716. [PMID: 31592161 PMCID: PMC6776071 DOI: 10.7717/peerj.7716] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/21/2019] [Indexed: 01/18/2023] Open
Abstract
Transcriptome sequencing data (6.5 Gb) of the salivary glands of the haematophagous leech Hirudo nipponia was obtained by using the BGIseq-500 platform. After identification and analysis, one transcript (Unigene5370) was annotated to hirudin HV3 from Hirudo medicinalis with an e-value of 1e-29 and was named hirudin-HN. This transcript was a new thrombin inhibitor gene belonging to the proteinase inhibitor I14 (hirudin) family. Hirudin-HN, with a 270-bp cDNA, encodes an 89-aa protein containing a 20-aa signal peptide. The mature hirudin-HN protein contains the typical structural characteristics of hirudin, e.g., three conserved disulfide bonds and the PKP and DFxxIP motifs. Proteins (Hir and M-Hir) were obtained via prokaryotic expression, and the mature hirudin-HN protein was shown to have anticoagulant activity and thrombin affinity by using the chromogenic substrate S2238 and surface plasmon resonance (SPR) interaction analysis, respectively. The N-terminal structure of the mature hirudin-HN protein was shown to be important for anticoagulant activity by comparing the activity and thrombin affinity of Hir and M-Hir. The abundances of Hirudin-HN mRNA and protein were higher in the salivary glands of starving animals than in those of feeding or fed leeches. These results provided a foundation for further study on the structure-function relationship of hirudin-HN with thrombin.
Collapse
Affiliation(s)
- Boxing Cheng
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China.,School of Biological Sciences, Guizhou Education University, Gui Yang, China
| | - Fei Liu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yan Cheng, China
| | - Qiaosheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China
| | - Yuxi Lu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China
| | - Hongzhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China
| | - Andong Ding
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China
| | - Chengfeng Xu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
22
|
Li T, Ma J, Xu Z, Wang S, Wang N, Shao S, Yang W, Huang L, Liu Y. Transcriptomic Analysis of the Influence of Methanol Assimilation on the Gene Expression in the Recombinant Pichia pastoris Producing Hirudin Variant 3. Genes (Basel) 2019; 10:genes10080606. [PMID: 31409011 PMCID: PMC6722669 DOI: 10.3390/genes10080606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Hirudin and its variants, as strong inhibitors against thrombin, are present in the saliva of leeches and are recognized as potent anticoagulants. However, their yield is far from the clinical requirement up to now. In this study, the production of hirudin variant 3 (HV3) was successfully realized by cultivating the recombinant Pichia pastoris GS115/pPIC9K-hv3 under the regulation of the promoter of AOX1 encoding alcohol oxidase (AOX). The antithrombin activity in the fermentation broth reached the maximum value of 5000 ATU/mL. To explore an effective strategy for improving HV3 production in the future, we investigated the influence of methanol assimilation on the general gene expression in this recombinant by transcriptomic study. The results showed that methanol was partially oxidized into CO2, and the rest was converted into glycerone-P which subsequently entered into central carbon metabolism, energy metabolism, and amino acid biosynthesis. However, the later metabolic processes were almost all down-regulated. Therefore, we propose that the up-regulated central carbon metabolism, energy, and amino acid metabolism should be beneficial for methanol assimilation, which would accordingly improve the production of HV3.
Collapse
Affiliation(s)
- Tao Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- College of Basic Science, Tianjin Agricultural University, Tianjin 300384, China
| | - Jieying Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zehua Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuang Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shulin Shao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wei Yang
- College of Basic Science, Tianjin Agricultural University, Tianjin 300384, China
| | - Lin Huang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| |
Collapse
|
23
|
Chen H, Cheng S, Fan F, Tu M, Xu Z, Du M. Identification and molecular mechanism of antithrombotic peptides from oyster proteins released in simulated gastro-intestinal digestion. Food Funct 2019; 10:5426-5435. [PMID: 31402368 DOI: 10.1039/c9fo01433k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, oyster (Crassostrea gigas) proteins were digested under in vitro gastrointestinal conditions to screen potential antithrombotic peptides. The sequences of the released peptides in the intestinal digestion phase were identified by ultra-performance liquid chromatography coupled to quadrupole time-of-flight MS (UPLC-Q-TOF-MS/MS). According to the antithrombotic activity analysis, the inhibitory ratio of oyster peptides showed an increasing trend, reaching up to 35.80% for a digestion period of 4 h. The APTT (activated partial thromboplastin time) and TT (thromboplastin time) were increased by oyster peptides for human serum in vitro. Oyster peptides showed a competitive inhibition effect on thrombin, based on Lineweaver-Burk plot analysis. Molecular docking between the antithrombotic peptides and thrombin (PDB: ) was conducted using Discovery Studio 2017. Potential inhibitors against thrombin and the mechanism of antithrombotic activity were predicted using the algorithm of CDOCKER. There are fourteen potential antithrombotic peptides, whose affinity with thrombin is higher than that of hirudin, as indicated by the "-CDOCKER energy" score (181.491). Peptide LSKEEIEEAKEV is similar in sequence to thrombin inhibitors. The binding sites of potential antithrombotic peptides against thrombin at the S1 pocket were compared with hirudin variant-2 (GDFEEIPEEYLQ). In addition, the peptides containing the RG/RGD sequence were identified, which can be hydrolyzed by thrombin as a substrate. Consequently, the oyster peptides released in simulated gastrointestinal digestion probably inhibit thrombin in two ways, not only as the inhibitor against the active site, but also as the substrate of thrombin. These results maybe be attributed to the potentially strong antithrombotic activity in the human digestive system.
Collapse
Affiliation(s)
- Hui Chen
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Shuzhen Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fengjiao Fan
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Maolin Tu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Zhe Xu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Ming Du
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| |
Collapse
|
24
|
Hirudins of the Asian medicinal leech, Hirudinaria manillensis: same same, but different. Parasitol Res 2019; 118:2223-2233. [DOI: 10.1007/s00436-019-06365-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/24/2019] [Indexed: 12/22/2022]
|
25
|
Müller C, Lukas P, Lemke S, Hildebrandt JP. Hirudin and Decorsins of the North American Medicinal Leech Macrobdella decora: Gene Structure Reveals Homology to Hirudins and Hirudin-Like Factors of Eurasian Medicinal Leeches. J Parasitol 2019. [DOI: 10.1645/18-117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Phil Lukas
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Sarah Lemke
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| |
Collapse
|
26
|
Cheng S, Tu M, Chen H, Xu Z, Wang Z, Liu H, Zhao G, Zhu B, Du M. Identification and inhibitory activity against α-thrombin of a novel anticoagulant peptide derived from oyster (Crassostrea gigas) protein. Food Funct 2019; 9:6391-6400. [PMID: 30457135 DOI: 10.1039/c8fo01635f] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A newly discovered anticoagulant peptide was isolated, purified and identified from the pepsin hydrolysate of oyster (Crassostrea gigas) which could potently prolong the activated partial thromboplastin time and the thrombin time. The anticoagulant peptide with a 1264.36 Da molecular mass was similar to the amino acid sequence of the C-terminal segment (DFEEIPEEYLQ) of hirudin (a potent thrombin inhibitor). The peptide specifically inhibited a vital blood coagulation factor: thrombin. The molecular docking energy scores of the anticoagulant peptide with the active site, exosite-I and exosite-II of thrombin were 132.355 kcal mol-1, 151.266 kcal mol-1 and 147.317 kcal mol-1, respectively. The anticoagulant peptide interacted with thrombin by competing with fibrinogen for an anion-binding exosite I. In the anticoagulant peptide-thrombin complex, there are seven hydrogen bonds and reciprocity exists between hydrogen atoms and oxygen atoms, and electrostatic and hydrophobic interactions are also involved. Such abundant interactions may be accountable for the high affinity and specificity of the anticoagulant peptide.
Collapse
Affiliation(s)
- Shuzhen Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Billur R, Sabo TM, Maurer MC. Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I. Biochemistry 2019; 58:1048-1060. [PMID: 30672691 DOI: 10.1021/acs.biochem.8b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thrombin, derived from zymogen prothrombin (ProT), is a serine protease involved in procoagulation, anticoagulation, and platelet activation. Thrombin's actions are regulated through anion-binding exosites I and II (ABE I and ABE II) that undergo maturation during activation. Mature ABEs can utilize exosite-based communication to fulfill thrombin functions. However, the conformational basis behind such long-range communication and the resultant ligand binding affinities are not well understood. Protease activated receptors (PARs), involved in platelet activation and aggregation, are known to target thrombin ABE I. Unexpectedly, PAR3 (44-56) can already bind to pro-ABE I of ProT. Nuclear magnetic resonance (NMR) ligand-enzyme titrations were used to characterize how individual PAR1 (49-62) residues interact with pro-ABE I and mature ABE I. 1D proton line broadening studies demonstrated that binding affinities for native PAR1P (49-62, P54) and for the weak binding variant PAR1G (49-62, P54G) increased as ProT was converted to mature thrombin. 1H,15N-HSQC titrations revealed that PAR1G residues K51, E53, F55, D58, and E60 exhibited less affinity to pro-ABE I than comparable residues in PAR3G (44-56, P51G). Individual PAR1G residues then displayed tighter binding upon exosite maturation. Long-range communication between thrombin exosites was examined by saturating ABE II with phosphorylated GpIbα (269-282, 3Yp) and monitoring the binding of PAR1 and PAR3 peptides to ABE I. Individual PAR residues exhibited increased affinities in this dual-ligand environment supporting the presence of interexosite allostery. Exosite maturation and beneficial long-range allostery are proposed to help stabilize an ABE I conformation that can effectively bind PAR ligands.
Collapse
Affiliation(s)
- Ramya Billur
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center , University of Louisville , Louisville , Kentucky 40202 , United States
| | - Muriel C Maurer
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| |
Collapse
|
28
|
Abstract
Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wide range of physiological processes and diseases. The existing and potential impacts of proteolysis-related activity on drug and biomarker development are presented in detail. All told the decisive roles of proteases in four major categories comprising 23 separate subcategories are addressed. Within this construct, 15 sets of subject-specific, tabulated data are presented that include identification of proteases, protease inhibitors, substrates, and their actions. Said data are derived from and confirmed by over 300 references. Cross comparison of datasets indicates that proteases, their inhibitors/promoters and substrates intersect over a range of physiological processes and diseases, both chronic and pathogenic. Indeed, "Proteases: Pivot Points …" closes by dramatizing this very point through association of (pro)Thrombin and Fibrin(ogen) with: hemostasis, innate immunity, cardiovascular and metabolic disease, cancer, neurodegeneration, and bacterial self-defense.
Collapse
Affiliation(s)
- Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sarah E Leonard
- Chemical and Biomolecular Engineering, University of Illinois Champaign-Urbana School of Chemical Sciences, Champaign, IL, USA
| | - Ray C Perkins
- New Liberty Proteomics Corporation, New Liberty, KY, USA.
| |
Collapse
|
29
|
Nastri F, Maglio O, Lombardi A. Vincenzo Pavone: Friend, mentor and inspiring scientist. Biopolymers 2018; 109:e23234. [PMID: 30394536 DOI: 10.1002/bip.23234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Flavia Nastri
- Department of Chemical Sciences, University of Napoli Federico II, Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Naples, Italy
| |
Collapse
|
30
|
De Filippis V, Pozzi N, Acquasaliente L, Artusi I, Pontarollo G, Peterle D. Protein engineering by chemical methods: Incorporation of nonnatural amino acids as a tool for studying protein folding, stability, and function. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Nicola Pozzi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Ilaria Artusi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| |
Collapse
|
31
|
Feng Y, Yin Z, Zhang D, Srivastava A, Ling C. Chinese Medicine Protein and Peptide in Gene and Cell Therapy. Curr Protein Pept Sci 2018; 20:251-264. [PMID: 29895243 DOI: 10.2174/1389203719666180612082432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 04/10/2018] [Accepted: 05/22/2018] [Indexed: 01/05/2023]
Abstract
The success of gene and cell therapy in clinic during the past two decades as well as our expanding ability to manipulate these biomaterials are leading to new therapeutic options for a wide range of inherited and acquired diseases. Combining conventional therapies with this emerging field is a promising strategy to treat those previously-thought untreatable diseases. Traditional Chinese medicine (TCM) has evolved for thousands of years in China and still plays an important role in human health. As part of the active ingredients of TCM, proteins and peptides have attracted long-term enthusiasm of researchers. More recently, they have been utilized in gene and cell therapy, resulting in promising novel strategies to treat both cancer and non-cancer diseases. This manuscript presents a critical review on this field, accompanied with perspectives on the challenges and new directions for future research in this emerging frontier.
Collapse
Affiliation(s)
- Yinlu Feng
- Department of Traditional Chinese Medicine, 401 Hospital of the Chinese People's Liberation Army, Qingdao, Shandong 266071, China.,Division of Cellular and Molecular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville 32611, FL, United States
| | - Zifei Yin
- Division of Cellular and Molecular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville 32611, FL, United States
| | - Daniel Zhang
- Division of Cellular and Molecular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville 32611, FL, United States
| | - Arun Srivastava
- Division of Cellular and Molecular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville 32611, FL, United States
| | - Chen Ling
- Division of Cellular and Molecular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville 32611, FL, United States
| |
Collapse
|
32
|
Sheffield WP, Eltringham-Smith LJ, Bhakta V. A factor XIa-activatable hirudin-albumin fusion protein reduces thrombosis in mice without promoting blood loss. BMC Biotechnol 2018; 18:21. [PMID: 29621998 PMCID: PMC5887181 DOI: 10.1186/s12896-018-0431-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/27/2018] [Indexed: 01/13/2023] Open
Abstract
Background Hirudin is a potent thrombin inhibitor but its antithrombotic properties are offset by bleeding side-effects. Because hirudin’s N-terminus must engage thrombin’s active site for effective inhibition, fusing a cleavable peptide at this site may improve hirudin’s risk/benefit ratio as a therapeutic agent. Previously we engineered a plasmin cleavage site (C) between human serum albumin (HSA) and hirudin variant 3 (HV3) in fusion protein HSACHV3. Because coagulation factor XI (FXI) is more involved in thrombosis than hemostasis, we hypothesized that making HV3 activity FXIa-dependent would also improve HV3’s potential therapeutic profile. We combined albumin fusion for half-life extension of hirudin with positioning of an FXIa cleavage site N-terminal to HV3, and assessed in vitro and in vivo properties of this novel protein. Results FXIa cleavage site EPR was employed. Fusion protein EPR-HV3HSA but not HSAEPR-HV3 was activated by FXIa in vitro. FVIIa, FXa, FXIIa, or plasmin failed to activate EPR-HV3HSA. FXIa-cleavable EPR-HV3HSA reduced the time to occlusion of ferric chloride-treated murine arteries and reduced fibrin deposition in murine endotoxemia; noncleavable mycHV3HSA was without effect. EPR-HV3HSA elicited less blood loss than constitutively active HV3HSA in murine liver laceration or tail transection but extended bleeding time to the same extent. EPR-HV3HSA was partially activated in citrated human or murine plasma to a greater extent than HSACHV3. Conclusions Releasing the N-terminal block to HV3 activity using FXIa was an effective way to limit hirudin’s bleeding side-effects, but plasma instability of the exposed EPR blocking peptide rendered it less useful than previously described plasmin-activatable HSACHV3.
Collapse
Affiliation(s)
- William P Sheffield
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada. .,Centre for Innovation, Canadian Blood Services, Hamilton, ON, Canada.
| | - Louise J Eltringham-Smith
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Varsha Bhakta
- Centre for Innovation, Canadian Blood Services, Hamilton, ON, Canada
| |
Collapse
|
33
|
De Filippis V, Acquasaliente L, Pontarollo G, Peterle D. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction. Biotechnol Appl Biochem 2018; 65:69-80. [DOI: 10.1002/bab.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| |
Collapse
|
34
|
Billur R, Ban D, Sabo TM, Maurer MC. Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I. Biochemistry 2017; 56:6343-6354. [PMID: 29111672 DOI: 10.1021/acs.biochem.7b00970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Thrombin participates in procoagulation, anticoagulation, and platelet activation. This enzyme contains anion binding exosites, ABE I and ABE II, which attract regulatory biomolecules. As prothrombin is activated to thrombin, pro-ABE I is converted into mature ABE I. Unexpectedly, certain ligands can bind to pro-ABE I specifically. Moreover, knowledge of changes in conformation and affinity that occur at the individual residue level as pro-ABE I is converted to ABE I is lacking. Such changes are transient and were not captured by crystallography. Therefore, we employed nuclear magnetic resonance (NMR) titrations to monitor development of ABE I using peptides based on protease-activated receptor 3 (PAR3). Proton line broadening NMR revealed that PAR3 (44-56) and more weakly binding PAR3G (44-56) could already interact with pro-ABE I on prothrombin. 1H-15N heteronuclear single-quantum coherence NMR titrations were then used to probe binding of individual 15N-labeled PAR3G residues (F47, E48, L52, and D54). PAR3G E48 and D54 could interact electrostatically with prothrombin and tightened upon thrombin maturation. The higher affinity for PAR3G D54 suggests the region surrounding thrombin R77a is better oriented to bind D54 than the interaction between PAR3G E48 and thrombin R75. Aromatic PAR3G F47 and aliphatic L52 both reported on significant changes in the chemical environment upon conversion of prothrombin to thrombin. The ABE I region surrounding the 30s loop was more affected than the hydrophobic pocket (F34, L65, and I82). Our NMR titrations demonstrate that PAR3 residues document structural rearrangements occurring during exosite maturation that are missed by reported X-ray crystal structures.
Collapse
Affiliation(s)
- Ramya Billur
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| |
Collapse
|
35
|
Pennington MW, Czerwinski A, Norton RS. Peptide therapeutics from venom: Current status and potential. Bioorg Med Chem 2017; 26:2738-2758. [PMID: 28988749 DOI: 10.1016/j.bmc.2017.09.029] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 12/19/2022]
Abstract
Peptides are recognized as being highly selective, potent and relatively safe as potential therapeutics. Peptides isolated from the venom of different animals satisfy most of these criteria with the possible exception of safety, but when isolated as single compounds and used at appropriate concentrations, venom-derived peptides can become useful drugs. Although the number of venom-derived peptides that have successfully progressed to the clinic is currently limited, the prospects for venom-derived peptides look very optimistic. As proteomic and transcriptomic approaches continue to identify new sequences, the potential of venom-derived peptides to find applications as therapeutics, cosmetics and insecticides grows accordingly.
Collapse
Affiliation(s)
| | - Andrzej Czerwinski
- Peptides International, Inc., 11621 Electron Drive, Louisville, KY 40299, USA
| | - Raymond S Norton
- Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Monash University, Parkville, 3052, Australia
| |
Collapse
|
36
|
Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem 2017; 38:1974-1979. [PMID: 28602026 PMCID: PMC5495612 DOI: 10.1002/jcc.24831] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/21/2017] [Accepted: 04/22/2017] [Indexed: 11/06/2022]
Abstract
The standard treatment of ions in the framework of the Poisson-Boltzmann equation relies on molecular surfaces, which are commonly constructed along with the Stern layer. The molecular surface determines where ions can be present. In the Gaussian-based smooth dielectric function in DelPhi, smooth boundaries between the solute and solvent take the place of molecular surface. Therefore, this invokes the question of how to model mobile ions in the water phase without a definite solute-solvent boundary. This article reports a natural extension of the Gaussian-based smooth dielectric function approach that treats mobile ions via Boltzmann distribution with an added desolvation penalty. Thus, ion concentration near macromolecules is governed by the local electrostatic potential and the desolvation penalty (from being partially desolvated). The approach is tested against the experimental salt dependence of binding free energy on 7 protein-protein complexes and 12 DNA-protein complexes, resulting in Pearson correlations of 0.95 and 0.88, respectively. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| |
Collapse
|
37
|
Kotick JD, Taghinia A. Prolonged Bleeding after a Single Leech Application in Pediatric Hand Surgery. J Hand Microsurg 2017; 9:98-100. [PMID: 28867911 DOI: 10.1055/s-0037-1604348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022] Open
Abstract
Use of the medicinal leech in microsurgery is common place for venous decongestion and can be associated with the need for transfusion over time and multiple applications. Here the authors present a case of profound, ongoing, life-threatening bleeding after a single leech application in pediatric microscopic surgery. There are no reports of such profound bleeding in the literature, and this case serves as a warning of the need for close surveillance in this subset of patients.
Collapse
Affiliation(s)
- James D Kotick
- Department of Plastic, Reconstructive, and Hand Surgery, Lahey Hospital and Medical Clinic, Tufts Medical School, Burlington, Massachusetts, United States
| | - Amir Taghinia
- Department of Plastic and Hand Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| |
Collapse
|
38
|
Pontarollo G, Acquasaliente L, Peterle D, Frasson R, Artusi I, De Filippis V. Non-canonical proteolytic activation of human prothrombin by subtilisin from Bacillus subtilis may shift the procoagulant-anticoagulant equilibrium toward thrombosis. J Biol Chem 2017; 292:15161-15179. [PMID: 28684417 DOI: 10.1074/jbc.m117.795245] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/28/2017] [Indexed: 12/26/2022] Open
Abstract
Blood coagulation is a finely regulated physiological process culminating with the factor Xa (FXa)-mediated conversion of the prothrombin (ProT) zymogen to active α-thrombin (αT). In the prothrombinase complex on the platelet surface, FXa cleaves ProT at Arg-271, generating the inactive precursor prethrombin-2 (Pre2), which is further attacked at Arg-320-Ile-321 to yield mature αT. Whereas the mechanism of physiological ProT activation has been elucidated in great detail, little is known about the role of bacterial proteases, possibly released in the bloodstream during infection, in inducing blood coagulation by direct proteolytic ProT activation. This knowledge gap is particularly concerning, as bacterial infections are frequently complicated by severe coagulopathies. Here, we show that addition of subtilisin (50 nm to 2 μm), a serine protease secreted by the non-pathogenic bacterium Bacillus subtilis, induces plasma clotting by proteolytically converting ProT into active σPre2, a nicked Pre2 derivative with a single cleaved Ala-470-Asn-471 bond. Notably, we found that this non-canonical cleavage at Ala-470-Asn-471 is instrumental for the onset of catalysis in σPre2, which was, however, reduced about 100-200-fold compared with αT. Of note, σPre2 could generate fibrin clots from fibrinogen, either in solution or in blood plasma, and could aggregate human platelets, either isolated or in whole blood. Our findings demonstrate that alternative cleavage of ProT by proteases, even by those secreted by non-virulent bacteria such as B. subtilis, can shift the delicate procoagulant-anticoagulant equilibrium toward thrombosis.
Collapse
Affiliation(s)
- Giulia Pontarollo
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Laura Acquasaliente
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Daniele Peterle
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Roberta Frasson
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Ilaria Artusi
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Vincenzo De Filippis
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| |
Collapse
|
39
|
Tian Q, Zhang P, Gao Z, Li H, Bai Z, Tan S. Hirudin as a novel fusion tag for efficient production of lunasin in Escherichia coli. Prep Biochem Biotechnol 2017; 47:619-626. [PMID: 28151045 DOI: 10.1080/10826068.2017.1286600] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fusion expression provides an effective means for the biosynthesis of longer peptides in Escherichia coli. However, the commonly used fusion tags are primarily suitable for laboratory scale applications due to the high cost of commercial affinity resins. Herein, a novel approach exploiting hirudin as a multipurpose fusion tag in combination with tobacco etch virus (TEV) protease cleavage has been developed for the efficient and cost-effective production of a 43-amino acid model peptide lunasin in E. coli at preparative scale. A fusion gene which allows for lunasin to be N-terminally fused to the C-terminus of hirudin through a flexible linker comprising a TEV protease cleavage site was designed and cloned in a secretion vector pTASH. By cultivation in a 7-L bioreactor, the fusion protein was excreted into the culture medium at a high yield of ~380 mg/L, which was conveniently recovered and purified by inexpensive HP20 hydrophobic chromatography at a recovery rate of ~80%. After polishing and cleavage with TEV protease, the finally purified lunasin was obtained with ≥95% purity and yield of ~86 mg/L culture medium. Conclusively, this hirudin tagging strategy is powerful in the production of lunasin and could be applicable for the production of other peptides at preparative scale.
Collapse
Affiliation(s)
- Qinghua Tian
- a Department of Molecular Biology, State Key Laboratory of Natural Medicines, School of Life Science and Technology , China Pharmaceutical University , Nanjing , P.R. China
| | - Ping Zhang
- a Department of Molecular Biology, State Key Laboratory of Natural Medicines, School of Life Science and Technology , China Pharmaceutical University , Nanjing , P.R. China
| | - Zhan Gao
- a Department of Molecular Biology, State Key Laboratory of Natural Medicines, School of Life Science and Technology , China Pharmaceutical University , Nanjing , P.R. China
| | - Hengli Li
- a Department of Molecular Biology, State Key Laboratory of Natural Medicines, School of Life Science and Technology , China Pharmaceutical University , Nanjing , P.R. China
| | - Zhengli Bai
- a Department of Molecular Biology, State Key Laboratory of Natural Medicines, School of Life Science and Technology , China Pharmaceutical University , Nanjing , P.R. China
| | - Shuhua Tan
- a Department of Molecular Biology, State Key Laboratory of Natural Medicines, School of Life Science and Technology , China Pharmaceutical University , Nanjing , P.R. China
| |
Collapse
|
40
|
Kouretova J, Hammamy MZ, Epp A, Hardes K, Kallis S, Zhang L, Hilgenfeld R, Bartenschlager R, Steinmetzer T. Effects of NS2B-NS3 protease and furin inhibition on West Nile and Dengue virus replication. J Enzyme Inhib Med Chem 2017; 32:712-721. [PMID: 28385094 PMCID: PMC6445162 DOI: 10.1080/14756366.2017.1306521] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
West Nile virus (WNV) and Dengue virus (DENV) replication depends on the viral NS2B-NS3 protease and the host enzyme furin, which emerged as potential drug targets. Modification of our previously described WNV protease inhibitors by basic phenylalanine analogs provided compounds with reduced potency against the WNV and DENV protease. In a second series, their decarboxylated P1-trans-(4-guanidino)cyclohexylamide was replaced by an arginyl-amide moiety. Compound 4-(guanidinomethyl)-phenylacetyl-Lys-Lys-Arg-NH2 inhibits the NS2B-NS3 protease of WNV with an inhibition constant of 0.11 µM. Due to the similarity in substrate specificity, we have also tested the potency of our previously described multibasic furin inhibitors. Their further modification provided chimeric inhibitors with additional potency against the WNV and DENV proteases. A strong inhibition of WNV and DENV replication in cell culture was observed for the specific furin inhibitors, which reduced virus titers up to 10,000-fold. These studies reveal that potent inhibitors of furin can block the replication of DENV and WNV.
Collapse
Affiliation(s)
- Jenny Kouretova
- a Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University , Marburg , Germany.,b German Center for Infection Research (DZIF) , University of Marburg , Marburg , Germany
| | - M Zouhir Hammamy
- a Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University , Marburg , Germany
| | - Anton Epp
- a Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University , Marburg , Germany
| | - Kornelia Hardes
- a Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University , Marburg , Germany
| | - Stephanie Kallis
- c Department of Infectious Diseases, Molecular Virology , Heidelberg University , Heidelberg , Germany
| | - Linlin Zhang
- d Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Lübeck , Germany.,e German Center for Infection Research (DZIF) , University of Lübeck , Lübeck , Germany
| | - Rolf Hilgenfeld
- d Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Lübeck , Germany.,e German Center for Infection Research (DZIF) , University of Lübeck , Lübeck , Germany
| | - Ralf Bartenschlager
- c Department of Infectious Diseases, Molecular Virology , Heidelberg University , Heidelberg , Germany.,f German Center for Infection Research (DZIF) , Heidelberg University , Heidelberg , Germany
| | - Torsten Steinmetzer
- a Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University , Marburg , Germany.,b German Center for Infection Research (DZIF) , University of Marburg , Marburg , Germany
| |
Collapse
|
41
|
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.
Collapse
Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | | | | | | | | | | |
Collapse
|
42
|
Guo SW, Du Y, Liu X. Endometriosis-Derived Stromal Cells Secrete Thrombin and Thromboxane A2, Inducing Platelet Activation. Reprod Sci 2016; 23:1044-52. [PMID: 26902428 DOI: 10.1177/1933719116630428] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Platelets have been recently revealed to play important roles in the development of endometriosis. However, it is unclear whether endometriotic lesions can secrete any platelet inducers outside the menstruation window. Hence, this study was undertaken to see whether endometriosis-derived stromal cells secrete platelet activators and cause platelet activation. We employed in vitro experimentation using primary ectopic endometrial stromal cells (EESCs) and platelets from healthy male volunteers and evaluated the extent of platelet aggregation by aggregometer and the platelet activation rate by flow cytometry using supernatants harvested from EESCs of different cell densities. We also measured the concentration of thromboxane B2 (TXB2), a metabolite of thromboxane A2 (TXA2), and thrombin activity in supernatants harvested from EESCs of different densities and evaluated the extent of platelet aggregation after treatment of EESCs with hirudin, Ozagrel, and apyrase. Finally, the concentration of TXB2, thrombin, and transforming growth factor β1 (TGF-β1) in platelets cocultured with different densities of EESCs is measured by enzyme-linked immunosorbent assay. We found that EESCs secrete thrombin and TXA2 and induce platelet activation and aggregation in a density-dependent fashion. Treatment of platelets with EESCs resulted in increased concentration of TXB2, thrombin, and TGF-β1 in a density-dependent manner. Treatment of EESCs with hirudin and Ozagrel, but not apyrase, resulted in significant suppression of platelet aggregation. Thus, given recently reported effects of activated platelets on the cell behaviors of EESCs and endometriotic lesions in general, our findings establish that endometriotic lesions and platelets engage active cross-talks in the development of endometriosis, highlighting the importance of lesion microenvironment in endometriosis.
Collapse
Affiliation(s)
- Sun-Wei Guo
- Shanghai Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Yanbo Du
- Shanghai Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China
| | - Xishi Liu
- Shanghai Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| |
Collapse
|
43
|
Azoulay Z, Rapaport H. The assembly state and charge of amphiphilic β-sheet peptides affect blood clotting. J Mater Chem B 2016; 4:3859-3867. [DOI: 10.1039/c6tb00330c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogels composed of designed β-sheet amphiphilic peptides have been exploited in several biomedical applications. Here the peptide's charge shows influence on blood compatibility with antithrombotic or no effects on clotting blood given by the anionic and zwitterionic peptides.
Collapse
Affiliation(s)
- Ziv Azoulay
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Hanna Rapaport
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nano-Science and Technology (IKI)
| |
Collapse
|
44
|
Asgari S, Mirzahoseini H, Karimipour M, Rahimi H, Ebrahim-Habibi A. Rational design of stable and functional hirudin III mutants with lower antigenicity. Biologicals 2015; 43:479-91. [DOI: 10.1016/j.biologicals.2015.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/12/2015] [Accepted: 07/23/2015] [Indexed: 12/25/2022] Open
|
45
|
Jablonka W, Kotsyfakis M, Mizurini DM, Monteiro RQ, Lukszo J, Drake SK, Ribeiro JMC, Andersen JF. Identification and Mechanistic Analysis of a Novel Tick-Derived Inhibitor of Thrombin. PLoS One 2015; 10:e0133991. [PMID: 26244557 PMCID: PMC4526366 DOI: 10.1371/journal.pone.0133991] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/04/2015] [Indexed: 12/05/2022] Open
Abstract
A group of peptides from the salivary gland of the tick Hyalomma marginatum rufipes, a vector of Crimean Congo hemorrhagic fever show weak similarity to the madanins, a group of thrombin-inhibitory peptides from a second tick species, Haemaphysalis longicornis. We have evaluated the anti-serine protease activity of one of these H. marginatum peptides that has been given the name hyalomin-1. Hyalomin-1 was found to be a selective inhibitor of thrombin, blocking coagulation of plasma and inhibiting S2238 hydrolysis in a competitive manner with an inhibition constant (Ki) of 12 nM at an ionic strength of 150 mM. It also blocks the thrombin-mediated activation of coagulation factor XI, thrombin-mediated platelet aggregation, and the activation of coagulation factor V by thrombin. Hyalomin-1 is cleaved at a canonical thrombin cleavage site but the cleaved products do not inhibit coagulation. However, the C-terminal cleavage product showed non-competitive inhibition of S2238 hydrolysis. A peptide combining the N-terminal parts of the molecule with the cleavage region did not interact strongly with thrombin, but a 24-residue fragment containing the cleavage region and the C-terminal fragment inhibited the enzyme in a competitive manner and also inhibited coagulation of plasma. These results suggest that the peptide acts by binding to the active site as well as exosite I or the autolysis loop of thrombin. Injection of 2.5 mg/kg of hyalomin-1 increased arterial occlusion time in a mouse model of thrombosis, suggesting this peptide could be a candidate for clinical use as an antithrombotic.
Collapse
Affiliation(s)
- Willy Jablonka
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland, United States of America
| | - Michalis Kotsyfakis
- Institute of Parasitology, Academy of Sciences of the Czech Republic, České Budejovice, Czech Republic
| | - Daniella M. Mizurini
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robson Q. Monteiro
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jan Lukszo
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Steven K. Drake
- Critical Care Medicine Department, Clinical Center; National Institutes of Health, Bethesda, Maryland, United States of America
| | - José M. C. Ribeiro
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland, United States of America
| | - John F. Andersen
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
| |
Collapse
|
46
|
Vogt AD, Chakraborty P, Di Cera E. Kinetic dissection of the pre-existing conformational equilibrium in the trypsin fold. J Biol Chem 2015. [PMID: 26216877 DOI: 10.1074/jbc.m115.675538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold.
Collapse
Affiliation(s)
- Austin D Vogt
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Pradipta Chakraborty
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| |
Collapse
|
47
|
Chen B, Soto AG, Coronel LJ, Goss A, van Ryn J, Trejo J. Characterization of thrombin-bound dabigatran effects on protease-activated receptor-1 expression and signaling in vitro. Mol Pharmacol 2015; 88:95-105. [PMID: 25934730 DOI: 10.1124/mol.114.096446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/30/2015] [Indexed: 12/15/2022] Open
Abstract
Thrombin, the key effector protease of the coagulation cascade, drives fibrin deposition and activates human platelets through protease-activated receptor-1 (PAR1). These processes are critical to the progression of thrombotic diseases. Thrombin is the main target of anticoagulant therapy, and major efforts have led to the discovery of new oral direct inhibitors of thrombin. Dabigatran is the first oral anticoagulant licensed for the prevention of thromboembolisms associated with orthopedic surgery and stroke prevention in atrial fibrillation. Dabigatran is a direct thrombin inhibitor that effectively blocks thrombin's catalytic activity but does not preclude thrombin's exosites and binding to fibrinogen. Thus, we hypothesized that catalytically inactive thrombin retains the capacity to bind to PAR1 through exosite-I and may modulate its function independent of receptor cleavage and activation. Here, we report that dabigatran at clinically relevant concentrations is an effective and acute inhibitor of thrombin-induced PAR1 cleavage, activation, internalization, and β-arrestin recruitment in vitro. Interestingly, prolonged exposure to catalytic inactive thrombin incubated with dabigatran at 20-fold higher therapeutic concentration resulted in increased PAR1 cell-surface expression, which correlated with higher detectable levels of ubiquitinated receptor. These findings are consistent with ubiquitin function as a negative regulator of PAR1 constitutive internalization. Increased PAR1 expression also enhanced agonist-induced phosphoinositide hydrolysis and endothelial barrier permeability. Thus, catalytically inactive thrombin appears to modulate PAR1 function in vitro by stabilizing receptor cell-surface expression; but given the high clearance rate of thrombin, the high concentration of dabigatran required to achieve this effect the in vivo physiologic relevance is unknown.
Collapse
Affiliation(s)
- Buxin Chen
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California (B.C., A.G.C., L.J.C., J.T.); Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (A.G.); and Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharma Gmbh, Biberach, Germany (J.R.)
| | - Antonio G Soto
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California (B.C., A.G.C., L.J.C., J.T.); Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (A.G.); and Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharma Gmbh, Biberach, Germany (J.R.)
| | - Luisa J Coronel
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California (B.C., A.G.C., L.J.C., J.T.); Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (A.G.); and Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharma Gmbh, Biberach, Germany (J.R.)
| | - Ashley Goss
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California (B.C., A.G.C., L.J.C., J.T.); Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (A.G.); and Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharma Gmbh, Biberach, Germany (J.R.)
| | - Joanne van Ryn
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California (B.C., A.G.C., L.J.C., J.T.); Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (A.G.); and Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharma Gmbh, Biberach, Germany (J.R.)
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California (B.C., A.G.C., L.J.C., J.T.); Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (A.G.); and Department of CardioMetabolic Disease Research, Boehringer Ingelheim Pharma Gmbh, Biberach, Germany (J.R.)
| |
Collapse
|
48
|
Lin L, Liu S, Nie Z, Chen Y, Lei C, Wang Z, Yin C, Hu H, Huang Y, Yao S. Automatic and Integrated Micro-Enzyme Assay (AIμEA) Platform for Highly Sensitive Thrombin Analysis via an Engineered Fluorescence Protein-Functionalized Monolithic Capillary Column. Anal Chem 2015; 87:4552-9. [DOI: 10.1021/acs.analchem.5b00723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Lihua Lin
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Shengquan Liu
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yingzhuang Chen
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Zhen Wang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Chao Yin
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Huiping Hu
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| |
Collapse
|
49
|
Multiple inhibitory kinetics reveal an allosteric interplay among thrombin functional sites. Thromb Res 2015; 135:212-6. [DOI: 10.1016/j.thromres.2014.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/20/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022]
|
50
|
Huang Y, Zhang Y, Zhao B, Xu Q, Zhou X, Song H, Yu M, Mo W. Structural basis of RGD-hirudin binding to thrombin: Tyr3 and five C-terminal residues are crucial for inhibiting thrombin activity. BMC STRUCTURAL BIOLOGY 2014; 14:26. [PMID: 25526801 PMCID: PMC4304120 DOI: 10.1186/s12900-014-0026-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 12/15/2014] [Indexed: 11/10/2022]
Abstract
Background Hirudin is an anti-coagulation protein produced by the salivary glands of the medicinal leech Hirudomedicinalis. It is a powerful and specific thrombin inhibitor. The novel recombinant hirudin, RGD-hirudin, which contains an RGD motif, competitively inhibits the binding of fibrinogen to GPIIb/IIIa on platelets, thus inhibiting platelet aggregation while maintaining its anticoagulant activity. Results Recombinant RGD-hirudin and six mutant variants (Y3A, S50A, Q53A, D55A, E57A and I59A), designed based on molecular simulations, were expressed in Pichia pastoris. The proteins were refolded and purified to homogeneity as monomers by gel filtration and anion exchange chromatography. The anti-thrombin activity of the six mutants and RGD-hirudin was tested. Further, we evaluated the binding of the mutant variants and RGD-hirudin to thrombin using BIAcore surface plasmon resonance analysis (SPR). Kinetics and affinity constants showed that the KD values of all six mutant proteins were higher than that of RGD-hirudin. Conclusions These findings contribute to a novel understanding of the interaction between RGD-hirudin and thrombin.
Collapse
Affiliation(s)
- Yinong Huang
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yanling Zhang
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Bing Zhao
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Qiping Xu
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Xiushi Zhou
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Houyan Song
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China. .,Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, China.
| | - Min Yu
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Wei Mo
- Key Laboratory of Metabolism and Molecular Medicine, ministry of education, Fudan University, Shanghai, China. .,The Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| |
Collapse
|