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Yi X, Liu J, Zang E, Tian Y, Liu J, Shi L. Exploring a Hirudin variant from nonhematophagous leeches: Unraveling full-length sequence, alternative splicing, function, and potential as a novel anticoagulant polypeptide. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118257. [PMID: 38677578 DOI: 10.1016/j.jep.2024.118257] [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: 02/29/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Leeches exhibit robust anticoagulant activity, making them useful for treating cardiovascular diseases in traditional Chinese medicine. Whitmania pigra, the primary source species of leech-derived medicinal compounds in China, has been demonstrated to possess formidable anticoagulant properties. Hirudin-like peptides, recognized as potent thrombin inhibitors, are prevalent in hematophagous leeches. Considering that W. pigra is a nonhematophagic leech, the following question arises: does a hirudin variant exist in this species? AIM OF THE STUDY In this study we identified the hirudin-encoding gene (WP_HV1) in the W. pigra genome. The goal of this study was to assess its anticoagulant activity and analyze the related mechanisms. MATERIALS AND METHODS In this study, a hirudin-encoding gene, WP_HV1, was identified from the W. pigra genome, and its accurate coding sequence (CDS) was validated through cloning from cDNA extracted from fresh W. pigra specimens. The structure of WP_HV1 and the amino acids associated with its anticoagulant activity were determined by sequence and structural analysis and prediction of its binding energy to thrombin. E. coli was used for the expression of WP_HV1 and recombinant proteins with various structures and mutants. The anticoagulant activity of the synthesized recombinant proteins was then confirmed using thrombin time (TT). RESULTS Validation of the WP_HV1 gene was accomplished, and three alternative splices were discovered. The TT of the blank sample exceeded that of the recombinant WP_HV1 sample by 1.74 times (0.05 mg/ml), indicating positive anticoagulant activity. The anticoagulant activity of WP_HV1 was found to be associated with its C-terminal tyrosine, along with the presence of 9 acidic amino acids on both the left and right sides. A significant reduction in the corresponding TT was observed for the mutated amino acids compared to those of the wild type, with decreases of 4.8, 6.6, and 3.9 s, respectively. In addition, the anticoagulant activity of WP_HV1 was enhanced and prolonged for 2.7 s when the lysine-67 residue was mutated to tryptophan. CONCLUSION Only one hirudin-encoding variant was identified in W. pigra. The active amino acids associated with anticoagulation in WP_HV1 were resolved and validated, revealing a novel source for screening and developing new anticoagulant drugs.
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Affiliation(s)
- Xiaozhe Yi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Jiali Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Erhuan Zang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yu Tian
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde 067000, China
| | - Jinxin Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China.
| | - Linchun Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China.
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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.
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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
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Shan H, Ren K, Liu J, Rehman SU, Yan X, Ma X, Zheng Y, Feng T, Wang X, Li Z, Zhou W, Chuang C, Liang M, Zheng J, Liu Q. Comprehensive Transcriptome Sequencing Analysis of Hirudinaria manillensis in Different Growth Periods. Front Physiol 2022; 13:897458. [PMID: 35694407 PMCID: PMC9174698 DOI: 10.3389/fphys.2022.897458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
Medical leeches are widely been used in biochemical and clinical medical studies, helping to restore blood circulation to grafted or severely injured tissue. Mostly, adult leeches are being used in the traditional pharmacopeia, but the gene expression profiling of leeches in different growth periods is not well-reported. So, in this study, we used transcriptome analysis to analyze the comparative gene expression patterns of Hirudinaria manillensis (H. manillensis) in different growth periods, including larval, young, and adult stages. We constructed 24 cDNA libraries from H. manillensis larval, young, and adult stages, and about 54,639,118 sequences were generated, 18,106 mRNA transcripts of which 958 novel mRNAs and 491 lncRNAs were also assembled as well. Furthermore, the results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the differentially upregulated genes from the larval to adult stages were enriched in pathways such as cilium, myofibril, contractile fiber, cytoskeleton proteins, dilated cardiomyopathy, adrenergic signaling in cardiomyocytes, etc. Moreover, in the adult stages, a significant increase in the expression of the Hirudin-HM (HIRM2) genes was detected. In addition, our comparative transcriptome profiling data from different growth stages of H. manillensis also identified a large number of DEGs and DElncRNAs which were tentatively found to be associated with the growth of H. manillensis; as it grew, the muscle-related gene expression increased, while the lipid metabolism and need for stimulation and nutrition-related genes decreased. Similarly, the higher expression of HIRM2 might attribute to the high expression of protein disulfide isomerase gene family (PDI) family genes in adulthood, which provides an important clue that why adult leeches rather than young leeches are widely used in clinical therapeutics and traditional Chinese medicine.
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Affiliation(s)
- Huiquan Shan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Ke Ren
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Jiasheng Liu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Xiaocong Ma
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Yalin Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Weiguan Zhou
- THAI Natural Hirudin Co., Ltd., Bangkok, Thailand
| | - Chen Chuang
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Mingkun Liang
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Jinghui Zheng
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Jinghui Zheng, ; Qingyou Liu,
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Jinghui Zheng, ; Qingyou Liu,
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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.
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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
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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.
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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
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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.
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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
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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
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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
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9
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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
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Betush RJ, Urban JM, Nilsson BL. Balancing hydrophobicity and sequence pattern to influence self-assembly of amphipathic peptides. Biopolymers 2018; 110. [PMID: 29292825 DOI: 10.1002/bip.23099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 01/25/2023]
Abstract
Amphipathic peptides with alternating polar and nonpolar amino acid sequences efficiently self-assemble into functional β-sheet fibrils as long as the nonpolar residues have sufficient hydrophobicity. For example, the Ac-(FKFE)2 -NH2 peptide rapidly self-assembles into β-sheet bilayer nanoribbons, while Ac-(AKAE)2 -NH2 fails to self-assemble under similar conditions due to the significantly reduced hydrophobicity and β-sheet propensity of Ala relative to Phe. Herein, we systematically explore the effect of substituting only two of the four Ala residues at various positions in the Ac-(AKAE)2 -NH2 peptide with amino acids of increasing hydrophobicity, β-sheet potential, and surface area (including Phe, 1-naphthylalanine (1-Nal), 2-naphthylalanine (2-Nal), cyclohexylalanine (Cha), and pentafluorophenylalanine (F5 -Phe)) on the self-assembly propensity of the resulting sequences. It was found that double Phe variants, regardless of the position of substitution, failed to self-assemble under the conditions used in this study. In contrast, all double 1-Nal and 2-Nal variants readily self-assembled, albeit at differing rates depending on the substitution patterns. To determine whether this was due to hydrophobicity or side chain surface area, we also prepared double Cha and F5 -Phe variant peptides (both side chain groups are more hydrophobic than Phe). Each of these variants also underwent effective self-assembly, with the aromatic F5 -Phe peptides doing so with greater efficiency. These findings provide insight into the role of amino acid hydrophobicity and sequence pattern on self-assembly proclivity of amphipathic peptides and on how targeted substitutions of nonpolar residues in these sequences can be exploited to tune the characteristics of the resulting self-assembled materials.
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Affiliation(s)
- Ria J Betush
- Department of Chemistry, Gannon University, Erie, Pennsylvania
| | - Jennifer M Urban
- Department of Chemistry, University of Rochester, Rochester, New York
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York
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12
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Pozzi N, Acquasaliente L, Frasson R, Cristiani A, Moro S, Banzato A, Pengo V, Scaglione GL, Arcovito A, De Cristofaro R, De Filippis V. β2 -Glycoprotein I binds to thrombin and selectively inhibits the enzyme procoagulant functions. J Thromb Haemost 2013; 11:1093-102. [PMID: 23578283 DOI: 10.1111/jth.12238] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 08/31/2023]
Abstract
BACKGROUND This work was aimed at characterizing the interaction of β(2)-glycoprotein I (β(2)GPI), an abundant plasma protein of unknown function, with human thrombin, the final effector protease in the coagulation cascade. METHODS The β(2)GPI-thrombin interaction was studied by surface plasmon resonance (SPR), fluorescence, and molecular modeling. The effect of β(2)GPI on the procoagulant (fibrin generation and platelet aggregation) and anticoagulant (protein C activation) functions of thrombin were investigated with turbidimetric, immunocytofluorimetric and enzymatic assays. RESULTS SPR and fluorescence data indicated that β(2)GPI tightly bound thrombin (K(d) = 34 nM) by interacting with both protease exosites, while leaving the active site accessible. This picture is fully consistent with the theoretical model of the β(2)GPI-thrombin complex. In particular, blockage of thrombin exosites with binders specific for exosite-1 (hirugen and HD1 aptamer) or exosite-2 (fibrinogen γ'-peptide and HD22 aptamer) impaired the β2 GPI-thrombin interaction. Identical results were obtained with thrombin mutants having one of the two exosites selectively compromised by mutation (Arg73Ala and Arg101Ala). Fluorescence measurements indicated that β(2)GPI did not affect the affinity of the enzyme for active site inhibitors, such as p-aminobenzamidine and the hirudin(1-47) domain, in agreement with the structural model. β(2)GPI dose-dependently prolonged the thrombin clotting time and ecarin clotting time in β(2)GPI-deficient plasma. β(2)GPI inhibited thrombin-induced platelet aggregation (IC50 = 0.36 μM) by impairing thrombin cleavage of protease-activated receptor 1 (PAR1) (IC50 = 0.32 μM), both on gel-filtered platelets and in whole blood. Strikingly, β(2) GPI did not affect thrombin-mediated generation of the anticoagulant protein C. CONCLUSIONS β(2) GPI functions as a physiologic anticoagulant by inhibiting the key procoagulant activities of thrombin without affecting its unique anticoagulant function.
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Affiliation(s)
- N Pozzi
- Laboratory of Protein Chemistry, School of Medicine, University of Padua, Padova, Italy
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Banzato A, Pozzi N, Frasson R, De Filippis V, Ruffatti A, Bison E, Padayattil S, Denas G, Pengo V. Antibodies to Domain I of β2Glycoprotein I are in close relation to patients risk categories in Antiphospholipid Syndrome (APS). Thromb Res 2011; 128:583-6. [DOI: 10.1016/j.thromres.2011.04.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/24/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
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14
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Thrombin inhibitors from different animals. J Biomed Biotechnol 2010; 2010:641025. [PMID: 20976270 PMCID: PMC2953280 DOI: 10.1155/2010/641025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 06/16/2010] [Accepted: 08/02/2010] [Indexed: 11/18/2022] Open
Abstract
Venous and arterial thromboembolic diseases are still the most frequent causes of death and disability in high-income countries. Clinical anticoagulants are inhibitors of enzymes involved in the coagulation pathway, such as thrombin and factor X(a). Thrombin is a key enzyme of blood coagulation system, activating the platelets, converting the fibrinogen to the fibrin net, and amplifying its self-generation by the activation of factors V, VIII, and XI. Thrombin has long been a target for the development of oral anticoagulants. Furthermore, selective inhibitors of thrombin represent a new class of antithrombotic agents. For these reasons, a number of specific thrombin inhibitors are under evaluation for possible use as antithrombotic drugs. This paper summarizes old and new interests of specific thrombin inhibitors described in different animals.
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De Filippis V, Frasson R, Fontana A. 3-Nitrotyrosine as a spectroscopic probe for investigating protein protein interactions. Protein Sci 2006; 15:976-86. [PMID: 16641485 PMCID: PMC2242503 DOI: 10.1110/ps.051957006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
3-Nitrotyrosine (NT) is approximately 10(3)-fold more acidic than Tyr, and its absorption properties are strongly pH-dependent. NT absorbs radiation in the wavelength range where Tyr and Trp emit fluorescence (300-450 nm), and it is essentially nonfluorescent. Therefore, NT may function as an energy acceptor in resonance energy transfer (FRET) studies for investigating ligand protein interactions. Here, the potentialities of NT were tested on the hirudin thrombin system, a well-characterized protease inhibitor pair of key pharmacological importance. We synthesized two analogs of the N-terminal domain (residues 1-47) of hirudin: Y3NT, in which Tyr3 was replaced by NT, and S2R/Y3NT, containing the substitutions Ser2 --> Arg and Tyr3 --> NT. The binding of these analogs to thrombin was investigated at pH 8 by FRET and UV/Vis-absorption spectroscopy. Upon hirudin binding, the fluorescence of thrombin was reduced by approximately 50%, due to the energy transfer occurring between the Trp residues of the enzyme (i.e., the donors) and the single NT of the inhibitor (i.e., the acceptor). The changes in the absorption spectra of the enzyme inhibitor complex indicate that the phenate moiety of NT in the free state becomes protonated to phenol in the thrombin-bound form. Our results indicate that the incorporation of NT can be effectively used to detect protein protein interactions with sensitivity in the low nanomolar range, to uncover subtle structural features at the ligand protein interface, and to obtain reliable Kd values for structure activity relationship studies. Furthermore, advances in chemical and genetic methods, useful for incorporating noncoded amino acids into proteins, highlight the broad applicability of NT in biotechnology and pharmacological screening.
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Affiliation(s)
- Vincenzo De Filippis
- Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, I-35131 Padua, Italy.
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16
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De Filippis V, De Dea E, Lucatello F, Frasson R. Effect of Na+ binding on the conformation, stability and molecular recognition properties of thrombin. Biochem J 2006; 390:485-92. [PMID: 15971999 PMCID: PMC1198928 DOI: 10.1042/bj20050252] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the present work, the effect of Na+ binding on the conformational, stability and molecular recognition properties of thrombin was investigated. The binding of Na+ reduces the CD signal in the far-UV region, while increasing the intensity of the near-UV CD and fluorescence spectra. These spectroscopic changes have been assigned to perturbations in the environment of aromatic residues at the level of the S2 and S3 sites, as a result of global rigidification of the thrombin molecule. Indeed, the Na+-bound form is more stable to urea denaturation than the Na+-free form by approximately 2 kcal/mol (1 cal identical with 4.184 J). Notably, the effects of cation binding on thrombin conformation and stability are specific to Na+ and parallel the affinity order of univalent cations for the enzyme. The Na+-bound form is even more resistant to limited proteolysis by subtilisin, at the level of the 148-loop, which is suggestive of the more rigid conformation this segment assumes in the 'fast' form. Finally, we have used hirudin fragment 1-47 as a molecular probe of the conformation of thrombin recognition sites in the fast and 'slow' form. From the effects of amino acid substitutions on the affinity of fragment 1-47 for the enzyme allosteric forms, we concluded that the specificity sites of thrombin in the Na+-bound form are in a more open and permissible conformation, compared with the more closed structure they assume in the slow form. Taken together, our results indicate that the binding of Na+ to thrombin serves to stabilize the enzyme into a more open and rigid conformation.
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Affiliation(s)
- Vincenzo De Filippis
- Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, via F. Marzolo 5, I-35131 Padua, Italy
- To whom correspondence should be addressed (email )
| | - Elisa De Dea
- Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, via F. Marzolo 5, I-35131 Padua, Italy
| | - Filippo Lucatello
- Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, via F. Marzolo 5, I-35131 Padua, Italy
| | - Roberta Frasson
- Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, via F. Marzolo 5, I-35131 Padua, Italy
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Frare E, de Laureto PP, Scaramella E, Tonello F, Marin O, Deana R, Fontana A. Chemical synthesis of the RGD-protein decorsin: Pro→Ala replacement reduces protein thermostability. Protein Eng Des Sel 2005; 18:487-95. [PMID: 16155118 DOI: 10.1093/protein/gzi054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Decorsin is a 39-residue polypeptide chain, crosslinked by three disulfide bridges, that strongly inhibits platelet aggregation. We report the chemical synthesis and characterization of analogs of decorsin with the aim of investigating the role of proline residues in protein structure, stability and biological activity. Decorsin analogs have been synthesized in which one (P23A and P24A decorsin) or two (P23,24A decorsin) proline residues have been substituted by alanine. The crude synthetic polypeptides were purified by reversed-phase HPLC in their reduced form and allowed to refold oxidatively to their disulfide-crosslinked species. The homogeneity of the synthetic mini-proteins, and also the correct pairing of the three disulfide bridges, were established by a number of analytical criteria, including fingerprinting analysis of the refolded synthetic analogs by using thermolysin and proteinase K as proteolytic enzymes. Replacement of proline by alanine results in a significant and cumulative decrease of the high thermal stability (Tm 74 degrees C) of native decorsin. The mono-substituted analogs display a Tm of 66-67 degrees C, while the double-substituted analog a Tm of 50 degrees C. On the other hand, the overall secondary and tertiary structures were not affected by the Pro-->Ala exchanges, as judged from circular dichroism measurements. Platelet aggregation assays established that the proline substitutions do not impair significantly the biological activity of decorsin. The results of this study clearly indicate that proline residues contribute significantly to the protein thermal stability. Our results are in line with the 'proline rule', previously advanced for explaining the unusual thermal stability of thermophilic enzymes, which usually show an enhanced content of proline residues with respect to their mesophilic counterparts.
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Affiliation(s)
- Erica Frare
- CRIBI Biotechnology Centre and Department of Biological Chemistry, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy
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18
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De Filippis V, De Boni S, De Dea E, Dalzoppo D, Grandi C, Fontana A. Incorporation of the fluorescent amino acid 7-azatryptophan into the core domain 1-47 of hirudin as a probe of hirudin folding and thrombin recognition. Protein Sci 2004; 13:1489-502. [PMID: 15152084 PMCID: PMC2279979 DOI: 10.1110/ps.03542104] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Revised: 02/17/2004] [Accepted: 02/18/2004] [Indexed: 10/26/2022]
Abstract
7-Azatryptophan (AW), a noncoded isostere of tryptophan (W), possesses interesting spectral properties. In particular, the presence of a nitrogen atom at position 7 in the indolyl nucleus of AW results in a red shift of the absorption maximum and fluorescence emission by 10 and 46 nm, respectively, compared to W. In the present work, we report the chemical synthesis and the conformational and functional characterization of an analog (denoted as Y3AW) of the N-terminal domain 1-47 of hirudin, a highly potent thrombin inhibitor, in which Tyr 3 has been replaced by AW. The results obtained were compared with those of the corresponding Y3W analog. We found that the replacement W --> AW reduces affinity for thrombin by 10-fold, likely because of the lower hydrophobicity of AW compared with that of W. Measurements of the resonance energy transfer effect, which was observed between Tyr13 and the amino acid at position 3 upon disulfide-coupled folding, demonstrate that AW behaves as a better energy acceptor than W for studying protein renaturation. The interaction of Y3AW with thrombin was studied by exciting the sample at 320 nm and recording the change in fluorescence of Y3AW on binding to the enzyme. Our results indicate that the fluorescence of AW of hirudin 1-47 in the Y3AW-thrombin complex is strongly quenched, possibly because of the presence of two structural water molecules at the hirudin-thrombin interface that can promote the nonradiative decay of AW in the excited state. The data herein reported demonstrate that the incorporation of AW can be of broad applicability in the study of protein folding and protein-protein interaction.
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Affiliation(s)
- Vincenzo De Filippis
- Department of Pharmaceutical Sciences, University of Padua, via F. Marzolo 5, I-35131 Padua, Italy.
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19
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Micheletti C, De Filippis V, Maritan A, Seno F. Elucidation of the disulfide-folding pathway of hirudin by a topology-based approach. Proteins 2004; 53:720-30. [PMID: 14579362 DOI: 10.1002/prot.10463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favor the progressive establishment of native interactions. At variance with traditional approaches based on native topology, not all native bonds are treated in the same way; in particular, a suitable energy term is introduced to account for the special strength of disulfide bonds, as well as their ability to undergo intramolecular reshuffling. The model thus possesses the minimal ingredients necessary to investigate the much debated issue of whether the refolding process occurs through partially structured intermediates with native or non-native disulfide bonds. This strategy is applied to a context of particular interest, the refolding process of hirudin, a thrombin-specific protease inhibitor, for which conflicting folding pathways have been proposed. We show that the only two parameters in the model (temperature and disulfide strength) can be tuned to reproduce well a set of experimental transitions between species with different number of formed disulfides. This model is then used to provide a characterization of the folding process and a detailed description of the species involved in the rate-limiting step of hirudin refolding.
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Affiliation(s)
- C Micheletti
- International School for Advanced Studies, INFM and the Abdus Salam Centre for Theoretical Physics, Trieste, Italy.
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20
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Abstract
Increased life expectancy is associated with aging populations in the developed countries, and we can expect an increased incidence of cardiovascular and inflammatory diseases and cancers. A priority for medical research is to reduce such morbidity. Leeches have been demonstrated to be a useful source of drugs to treat cardiovascular diseases, as they have evolved highly specific mechanisms to feed on their hosts by blocking blood coagulation. Powerful molecules acting at different points in the coagulation cascade or in the inhibition of platelet aggregation have been purified from these animals. Moreover, clinical trials confirm their potential to treat cardiovascular diseases.
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Affiliation(s)
- M Salzet
- Laboratoire d'Endocrinologie et Immunité des Annélides, UPRESA CNRS 8017, Université des Sciences et Technologies de Lille, SN3, F-59655 Cedex, Villeneuve d'Ascq, France.
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21
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Salzet M, Chopin V, Baert J, Matias I, Malecha J. Theromin, a novel leech thrombin inhibitor. J Biol Chem 2000; 275:30774-80. [PMID: 10837466 DOI: 10.1074/jbc.m000787200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We purified the most potent thrombin inhibitor described to date from the rhynchobdellid leech Theromyzon tessulatum. Designated theromin, it was purified to apparent homogeneity by gel permeation and anion exchange chromatography followed by two reverse-phase steps of high performance liquid chromatography. The primary sequence of theromin (a homodimer of 67 amino acid residues including 16 cysteine residues) was determined by a combination of reduction and s-beta-pyridylethylation, Edman degradation, trypsin enzymatic digestion, and matrix-assisted laser desorption mass spectrometry measurement. Theromin exhibits no sequence homology with any other thrombin inhibitors. Furthermore, theromin significantly diminishes, in a dose-dependent manner, the level of human granulocyte and monocyte activation induced by lipopolysaccharides. In summary, this potent thrombin inhibitor promises to have high biomedical significance.
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Affiliation(s)
- M Salzet
- Laboratoire d'Endocrinologie des Annélides, Unité Propre de la Recherche Supérieure Associée au CNRS 8017 CNRS, SN3, Université des Sciences et Technologie de Lille, F-59655 Villeneuve d'Ascq Cedex, France.
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22
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Abstract
A large number of potent and selective therapeutic agents, useful for the treatment of several diseases, have been isolated from natural sources. For example, the most active thrombin inhibitors are those secreted by the salivary glands of leeches. One peculiar feature of these agents is the lack of any significant inhibitory cross-reaction with other serine proteinases. Hence, the knowledge of the exact mechanism of action of these molecules provides the basis for the development of new and efficient synthetic drugs. For this reason, many studies have been undertaken on the structure-activity relationships of natural thrombin inhibitors, and a large amount of detailed information has been obtained by the crystal structures of these inhibitors when complexed with thrombin. In this paper, we review natural and synthetic multisite thrombin inhibitors, whose structural aspects have been determined in detail. We also report here the approach used by us to develop a new class of synthetic, multisite directed thrombin inhibitors, named hirunorms, designed to mimic the distinctive binding mode of hirudin.
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Affiliation(s)
- A Lombardi
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Napoli Federico II, Italy
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23
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Liu G, Mu SF, Yun LH, Ding ZK, Sun MJ. Systematic study of the substituted active C-terminus of hirudin. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 54:480-90. [PMID: 10604593 DOI: 10.1034/j.1399-3011.1999.00132.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hirudin, a potent clinical thrombin inhibitor from Hirudo medicinalis, consists of 65 amino acids in a single chain. In this paper, we systematically synthesize a series of C-terminal (desulfo hirudin45-65) peptides substituted by 20 natural L-amino acids via the Multipin method. The resulting peptide library is subsequently screened using an alpha-thrombin-mediated fibrinogen clotting assay and alpha-thrombin-induced amidolytic hydrolysis assay.
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Affiliation(s)
- G Liu
- Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, China.
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24
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De Filippis V, Russo I, Vindigni A, Di Cera E, Salmaso S, Fontana A. Incorporation of noncoded amino acids into the N-terminal domain 1-47 of hirudin yields a highly potent and selective thrombin inhibitor. Protein Sci 1999; 8:2213-7. [PMID: 10548068 PMCID: PMC2144148 DOI: 10.1110/ps.8.10.2213] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Hirudin is an anticoagulant polypeptide isolated from a medicinal leech that inhibits thrombin with extraordinary potency (Kd = 0.2-1.0 pM) and selectivity. Hirudin is composed of a compact N-terminal region (residues 1-47, cross-linked by three disulfide bridges) that binds to the active site of thrombin, and a flexible C-terminal tail (residues 48-64) that interacts with the exosite I of the enzyme. To minimize the sequence of hirudin able to bind thrombin and also to improve its therapeutic profile, several N-terminal fragments have been prepared as potential anticoagulants. However, the practical use of these fragments has been impaired by their relatively poor affinity for the enzyme, as given by the increased value of the dissociation constant (Kd) of the corresponding thrombin complexes (Kd = 30-400 nM). The aim of the present study is to obtain a derivative of the N-terminal domain 1-47 of hirudin displaying enhanced inhibitory potency for thrombin compared to the natural product. In this view, we have synthesized an analogue of fragment 1-47 of hirudin HM2 in which Val1 has been replaced by tert-butylglycine, Ser2 by Arg, and Tyr3 by beta-naphthylalanine, to give the BugArgNal analogue. The results of chemical and conformational characterization indicate that the synthetic peptide is able to fold efficiently with the correct disulfide topology (Cys6-Cys14, Cys16-Cys28, Cys22-Cys37), while retaining the conformational properties of the natural fragment. Thrombin inhibition data indicate that the effects of amino acid replacements are perfectly additive if compared to the singly substituted analogues (De Filippis V, Quarzago D, Vindigni A, Di Cera E, Fontana A, 1998, Biochemistry 37:13507-13515), yielding a molecule that inhibits the fast or slow form of thrombin by 2,670- and 6,818-fold more effectively than the natural fragment, and that binds exclusively at the active site of the enzyme with an affinity (Kd,fast = 15.4 pM, Kd,slow = 220 pM) comparable to that of full-length hirudin (Kd,fast = 0.2 pM, Kd,slow = 5.5 pM). Moreover, BugArgNal displays absolute selectivity for thrombin over the other physiologically important serine proteases trypsin, plasmin, factor Xa, and tissue plasminogen activator, up to the highest concentration of inhibitor tested (10 microM).
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Affiliation(s)
- V De Filippis
- CRIBI Biotechnology Center and Department of Pharmaceutical Sciences, University of Padua, Italy
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25
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Di Cera E. Site-Specific Thermodynamics: Understanding Cooperativity in Molecular Recognition. Chem Rev 1998; 98:1563-1592. [PMID: 11848942 DOI: 10.1021/cr960135g] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, Missouri 63110
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26
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di Cera E. Site-specific analysis of mutational effects in proteins. ADVANCES IN PROTEIN CHEMISTRY 1998; 51:59-119. [PMID: 9615169 DOI: 10.1016/s0065-3233(08)60651-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- E di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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27
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Polverino de Laureto P, Scaramella E, De Filippis V, Marin O, Doni MG, Fontana A. Chemical synthesis and structural characterization of the RGD-protein decorsin: a potent inhibitor of platelet aggregation. Protein Sci 1998; 7:433-44. [PMID: 9521121 PMCID: PMC2143916 DOI: 10.1002/pro.5560070225] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Decorsin is a 39-residue RGD-protein crosslinked by three disulfide bridges isolated from the leech Macrobdella decora belonging to the family of GPIIb-IIIa antagonists and acting as a potent inhibitor of platelet aggregation. Here we report the solid-phase synthesis of decorsin using the Fmoc strategy. The crude polypeptide was purified by reverse-phase HPLC in its reduced form and allowed to refold in the presence of glutathione. The homogeneity of the synthetic oxidized decorsin was established by reverse-phase HPLC and capillary zone electrophoresis. The results of amino acid analysis after acid hydrolysis of the synthetic protein, NH2-terminal sequencing and mass determination (4,377 Da) by electrospray mass spectrometry were in full agreement with this theory. The correct pairing of the three disulfide bridges in synthetic decorsin was determined by a combined approach of both peptide mapping using proteolytic enzymes and analysis of the disulfide chirality by CD spectroscopy in the near-UV region. Synthetic decorsin inhibited human platelet aggregation with an IC50 of approximately 0.1 microM, a figure quite similar to that determined utilizing decorsin from natural source. In particular, the synthetic protein was 2,000-fold more potent than a model RGD-peptide (e.g., Arg-Gly-Asp-Ser) in inhibiting platelet aggregation. Thermal denaturation experiments of synthetic decorsin, monitored by CD spectroscopy, revealed its high thermal stability (Tm approximately 74 degrees C). The features of the oxidative refolding process of reduced decorsin, as well as the thermal stability of the oxidized species, were compared with those previously determined for the NH2-terminal core domain fragment 1-41 or 1-43 from hirudin. This fragment shows similarity in size, pairing of the three disulfides and three-dimensional structure with those of decorsin, even if very low sequence similarity. It is suggested that the less efficient oxidative folding and the enhanced thermal stability of decorsin in respect to those of hirudin core domain likely can be ascribed to the presence of the six Pro residues in the decorsin chain, whereas none is present in the hirudin domain. The results of this study indicate that decorsin can be obtained by solid-phase methodology in purity and quantities suitable for structural and functional studies and thus open the way to prepare by chemical methods novel decorsin derivatives containing unusual amino acids or even non-peptidic moieties.
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Fusi P, Goossens K, Consonni R, Grisa M, Puricelli P, Vecchio G, Vanoni M, Zetta L, Heremans K, Tortora P. Extreme heat- and pressure-resistant 7-kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single-point amino acid substitution. Proteins 1997; 29:381-90. [PMID: 9365992 DOI: 10.1002/(sici)1097-0134(199711)29:3<381::aid-prot11>3.0.co;2-j] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study reports the characterization of the recombinant 7-kDa protein P2 from Sulfolobus solfataricus and the mutants F31A and F31Y with respect to temperature and pressure stability. As observed in the NMR, FTIR, and CD spectra, wild-type protein and mutants showed substantially similar structures under ambient conditions. However, midpoint transition temperatures of the denaturation process were 361, 334, and 347 K for wild type, F31A, and F31Y mutants, respectively: thus, alanine substitution of phenylalanine destabilized the protein by as much as 27 K. Midpoint transition pressures for wild type and F31Y mutant could not be accurately determined because they lay either beyond (wild type) or close to (F31Y) 14 kbar, a pressure at which water undergoes a phase transition. However, a midpoint transition pressure of 4 kbar could be determined for the F31A mutant, implying a shift in transition of at least 10 kbar. The pressure-induced denaturation was fully reversible; in contrast, thermal denaturation of wild type and mutants was only partially reversible. To our knowledge, both the pressure resistance of protein P2 and the dramatic pressure and temperature destabilization of the F31A mutant are unprecedented. These properties may be largely accounted for by the role of an aromatic cluster where Phe31 is found at the core, because interactions among aromatics are believed to be almost pressure insensitive; furthermore, the alanine substitution of phenylalanine should create a cavity with increased compressibility and flexibility, which also involves an impaired pressure and temperature resistance.
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Affiliation(s)
- P Fusi
- Dipartimento di Fisiologia e Biochimica generali, Università di Milano, Italy
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29
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Vindigni A, Dang QD, Di Cera E. Site-specific dissection of substrate recognition by thrombin. Nat Biotechnol 1997; 15:891-5. [PMID: 9306406 DOI: 10.1038/nbt0997-891] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Current approaches to enzyme specificity focus on the identification of consensus sequences from combinatorial chemistry libraries or phage display. These synthetic substrates can also be used as sensitive probes for the molecular environment of the enzyme specificity sites to determine how they contribute to recognition in the transition state. Libraries constructed to include all relevant species for a site-specific analysis contain a relatively small number of substrates and provide quantitative information on the energetics of recognition that can be exploited in studies of structure-function relations and rational drug design. We have constructed a library of substrates carrying substitutions at P1, P2, and P3 to probe the response of the specificity sites S1, S2, and S3 of thrombin. The library has been used to identify differences between the anticoagulant slow and procoagulant fast forms of thrombin and the structural origin of the effects. The results also offer new guidelines for the design of active-site inhibitors of thrombin.
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Affiliation(s)
- A Vindigni
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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de Bernard M, Papini E, de Filippis V, Gottardi E, Telford J, Manetti R, Fontana A, Rappuoli R, Montecucco C. Low pH activates the vacuolating toxin of Helicobacter pylori, which becomes acid and pepsin resistant. J Biol Chem 1995; 270:23937-40. [PMID: 7592587 DOI: 10.1074/jbc.270.41.23937] [Citation(s) in RCA: 163] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The protein toxin VacA, produced by cytotoxic strains of Helicobacter pylori, causes a vacuolar degeneration of cells, which eventually die. VacA is strongly activated by a short exposure to acidic solutions in the pH 1.5-5.5 range, followed by neutralization. Activated VacA has different CD and fluorescence spectra and a limited proteolysis fragmentation pattern from VacA kept at neutral pH. Moreover, activated VacA is resistant to pH 1.5 and to pepsin. The relevance of these findings to pathogenesis of H. pylori-induced gastrointestinal ulcers is discussed.
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Affiliation(s)
- M de Bernard
- Centro Consiglio Nazionale delle Ricerche di Biomembrane, Università di Padova, Italy
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