Anti-haemostatic compounds from the vampire snail Cumia reticulata: Molecular cloning and in-silico structure-function analysis.

Abstract:

:Blood-feeding animals are known for their ability to produce bioactive compounds to impair haemostasis and suppress pain perception in the host. These compounds are extremely appealing for pharmacological development since they are generally very effective and specific for their molecular target. A preliminary RNA-Seq based characterization of the secretion from salivary and mid-oesophageal tissues of the vampire snail Cumia reticulata, revealed a complex mixture of feeding-related transcripts with potential anaesthetic and anticoagulant action. Based on the cloned full-length mRNAs, it was possible to verify the sequence of five genes encoding haematophagy-related products. The in silico modelled three-dimensional structure of each translational product was analysed to gain information on their potential biochemical activity. We have hereby validated and further investigated the assembled transcripts presumably involved in the antihaemostatic action, to improve our comprehensive understanding of this subset of the feeding secretion. The studied proteins included both inhibitors of primary haemostasis such as the vWFA domain-containing proteins, and compounds targeting different steps of the coagulation cascade, as e.g. the Turripeptide-like/protease inhibitor, the TFPI-like multiple Kunitz-type protease inhibitors, the Meprin-like metalloproteases and the Astacin/ShKT-like domain-containing proteins. All these molecules showed promising potential for pharmacological development.

journal_name

Comput Biol Chem

authors

Modica MV,Reinoso Sánchez J,Pasquadibisceglie A,Oliverio M,Mariottini P,Cervelli M

doi

10.1016/j.compbiolchem.2018.05.014

subject

Has Abstract

pub_date

2018-08-01 00:00:00

pages

168-177

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(18)30225-1

journal_volume

75

pub_type

杂志文章
  • A vibrational entropy term for DNA docking with autodock.

    abstract::DNA interacts with small molecules, from water to endogenous reactive oxygen and nitrogen species, environmental mutagens and carcinogens, and pharmaceutical anticancer molecules. Understanding and predicting the physical interactions of small molecules with DNA via docking is key not only for the comprehension of mol...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.03.027

    authors: McElfresh GW,Deligkaris C

    更新日期:2018-06-01 00:00:00

  • Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization.

    abstract::The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational cha...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2007.02.005

    authors: Zhang Y,Zheng N,Zhong Y

    更新日期:2007-04-01 00:00:00

  • C3: An R package for cross-species compendium-based cell-type identification.

    abstract::Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples becau...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.10.003

    authors: Kabir MH,Djordjevic D,O'Connor MD,Ho JWK

    更新日期:2018-12-01 00:00:00

  • GeneMCL in microarray analysis.

    abstract::Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edg...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2005.07.002

    authors: Samuel Lattimore B,van Dongen S,Crabbe MJ

    更新日期:2005-10-01 00:00:00

  • Computational identification of novel microRNA homologs in the chimpanzee genome.

    abstract::MicroRNAs are important negative regulators of gene expression in higher eukaryotes. The miRNA repertoire of the closest human animal relative, the chimpanzee (Pan troglodytes), is largely unknown. In this study, we focused on computational search of novel miRNA homologs in chimpanzee. We have searched and analyzed th...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.07.024

    authors: Baev V,Daskalova E,Minkov I

    更新日期:2009-02-01 00:00:00

  • Theoretical aspects of 13C metabolic flux analysis with sole quantification of carbon dioxide labeling.

    abstract::The potential of using sole respirometric CO2 labeling measurement for 13C metabolic flux analysis was investigated by metabolic simulations. For this purpose a model was created, considering all CO2 forming and consuming reactions in the central catabolic and anabolic pathways. To facilitate the interpretation of the...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2005.02.005

    authors: Yang TH,Heinzle E,Wittmann C

    更新日期:2005-04-01 00:00:00

  • Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature.

    abstract::Bio-entity name recognition is the key step for information extraction from biomedical literature. This paper presents a dictionary-based bio-entity name recognition approach. The approach expands the bio-entity name dictionary via the Abbreviation Definitions identifying algorithm, improves the recall rate through th...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.03.008

    authors: Yang Z,Lin H,Li Y

    更新日期:2008-08-01 00:00:00

  • Comprehensive comparison of two protein family of P-ATPases (13A1 and 13A3) in insects.

    abstract::The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of ...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.04.006

    authors: Seddigh S

    更新日期:2017-06-01 00:00:00

  • Immunopeptidome screening to design An immunogenic construct against PRAME positive breast cancer; An in silico study.

    abstract:BACKGROUND:Metastasis is the main cause of breast cancer (BC) lethality, especially in early stages, led to improvements in therapeutic procedures. Lately, by improvements in our perception of biological processes and immune system new classes of vaccines are emerged that grant us the opportunity of designing resolute ...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2020.107231

    authors: Afzali F,Minuchehr Z,Jahangiri S,Ranjbar MM

    更新日期:2020-04-01 00:00:00

  • Conformational difference between two subunits in flavin mononucleotide binding protein dimers from Desulfovibrio vulgaris (MF): molecular dynamics simulation.

    abstract::The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, su...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.05.007

    authors: Nunthaboot N,Lugsanangarm K,Pianwanit S,Kokpol S,Tanaka F,Nakanishi T,Kitamura M

    更新日期:2016-10-01 00:00:00

  • Multilocus consensus genetic maps (MCGM): formulation, algorithms, and results.

    abstract::In process of creating genetic maps different labs/research groups obtain overlapping parts of the map. Merging these parts into one integrative map is based on looking for maximum shared marker orders among the maps. Really, not all shared markers of such maps have consensus order that obstructs building of the integ...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2005.09.007

    authors: Mester DI,Ronin YI,Korostishevsky MA,Pikus VL,Glazman AE,Korol AB

    更新日期:2006-02-01 00:00:00

  • Chromatographic and computational screening of anisotropic lipophilicity and pharmacokinetics of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimides.

    abstract::The present study is focused on a series of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimide derivatives, as potential anticonvulsants. The retention behavior of eleven succinimide derivatives was determined by using reversed phase high performance liquid chromatography (RP-HPLC) and reversed phase high performanc...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107161

    authors: Kovačević S,Banjac MK,Podunavac-Kuzmanović S,Milošević N,Ćurčić J,Vulić J,Šeregelj V,Banjac N,Ušćumlić G

    更新日期:2020-02-01 00:00:00

  • GADS software for parametric linkage analysis of quantitative traits distributed as a point-mass mixture.

    abstract::Often the quantitative data coming from proteomics and metabolomics studies have irregular distribution with a spike. None of the wide used methods for human QTL mapping are applicable to such traits. Researchers have to reduce the sample, excluding the spike, and analyze only continuous measurements. In this study, w...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2011.11.004

    authors: Axenovich TI,Zorkoltseva IV

    更新日期:2012-02-01 00:00:00

  • The binding mode of picrotoxinin in GABAA-ρ receptors: Insight into the subunit's selectivity in the transmembrane domain.

    abstract::The channel blocker picrotoxinin has been studied with GABAA-ρ1 and GABAA-ρ2 homology models based on the GluCl crystal structure. Picrotoxinin is tenfold more potent for GABAA-ρ2 than for GABAA-ρ1 homomeric channels. This intra-subunit selectivity arises from the unconserved residues at the 2' sites, which are the es...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.07.003

    authors: Naffaa MM,Samad A

    更新日期:2016-10-01 00:00:00

  • Genome-wide identification and expression analysis of SWI1 genes in Boechera species.

    abstract::As a mode of reproduction in plants, apomixis leads to the generation of clones via seeds. Apomictic plants form viable diploid female gametes without meiosis (apomeiosis) and produce embryos without fertilization (parthenogenesis). Apomeiosis, as a major component of apomixis, has recently been reported in some Arabi...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.04.004

    authors: Sezer F,Yüzbaşioğlu G,Özbilen A,Taşkin KM

    更新日期:2016-06-01 00:00:00

  • Domain boundary prediction based on profile domain linker propensity index.

    abstract::Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensit...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2006.01.001

    authors: Dong Q,Wang X,Lin L,Xu Z

    更新日期:2006-04-01 00:00:00

  • Synthesis, monoamine oxidase inhibitory activity and computational study of novel isoxazole derivatives as potential antiparkinson agents.

    abstract::Monoamine oxidase (MAO) enzymes are one of the most promising targets for the treatment of neurological disorders. A series of phenylisoxazole carbohydrazides was designed, synthesized and screened for both MAO-A and MAO-B inhibition using Amplex Red assays. None of the compounds inhibited the MAO-A activity while mos...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.01.012

    authors: Agrawal N,Mishra P

    更新日期:2019-04-01 00:00:00

  • Discovery of potential Zika virus RNA polymerase inhibitors by docking-based virtual screening.

    abstract::Zika virus (ZIKV) infection has been associated with Guillain-Barre syndrome in adults and microcephaly in infants. The existence of insufficient structural data in most of the protein databases hinders the synthesis of anti-ZIKV pharmaceutics. In this work, we attempted to model the catalytic domain of the ZIKV RNA p...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.10.007

    authors: Singh A,Jana NK

    更新日期:2017-12-01 00:00:00

  • Identification of possible siRNA molecules for TDP43 mutants causing amyotrophic lateral sclerosis: In silico design and molecular dynamics study.

    abstract::The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a syst...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.01.001

    authors: Bhandare VV,Ramaswamy A

    更新日期:2016-04-01 00:00:00

  • Drug-target interaction prediction by integrating multiview network data.

    abstract::Drug-target interaction (DTI) prediction is a challenging step in further drug repositioning, drug discovery and drug design. The advent of high-throughput technologies brings convenience to the development of DTI prediction methods. With the generation of a high number of data sets, many mathematical models and compu...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.03.011

    authors: Zhang X,Li L,Ng MK,Zhang S

    更新日期:2017-08-01 00:00:00

  • Protein function prediction using neighbor relativity in protein-protein interaction network.

    abstract::There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interact...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2012.12.003

    authors: Moosavi S,Rahgozar M,Rahimi A

    更新日期:2013-04-01 00:00:00

  • Ambush hypothesis revisited: Evidences for phylogenetic trends.

    abstract::Recoding events occur in competition with standard readout of the transcript, and are site-specific. Recoding is the reprogramming of mRNA translation by localized alterations in the standard translational rules. Frame-shifting is one class of recoding and defined as protein translations that start not at the first, b...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2009.04.002

    authors: Singh TR,Pardasani KR

    更新日期:2009-06-01 00:00:00

  • Computational insight into dengue virus NS2B-NS3 protease inhibition: A combined ligand- and structure-based approach.

    abstract::The NS2B-NS3 protease is essential for the replication process of Dengue Virus, which make it an attractive target for anti-virus drugs. Since a considerable number of NS2B-NS3 protease inhibitors have been reported so far, it is significant for the discovery of more effective antivirus compounds with the essential st...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.09.010

    authors: Chen J,Jiang H,Li F,Hu B,Wang Y,Wang M,Wang J,Cheng M

    更新日期:2018-12-01 00:00:00

  • An unusual 500,000 bases long oscillation of guanine and cytosine content in human chromosome 21.

    abstract::An oscillation with a period of around 500 kb in guanine and cytosine content (GC%) is observed in the DNA sequence of human chromosome 21. This oscillation is localized in the rightmost one-eighth region of the chromosome, from 43.5 Mb to 46.5 Mb. Five cycles of oscillation are observed in this region with six GC-ric...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2004.09.011

    authors: Li W,Holste D

    更新日期:2004-12-01 00:00:00

  • Self-organizing map of gene regulatory networks for cell phenotypes during reprogramming.

    abstract::The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflec...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2011.05.002

    authors: Zhang L,Zheng Y,Li D,Zhong Y

    更新日期:2011-08-10 00:00:00

  • Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen.

    abstract::Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the pos...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107166

    authors: Manish M,Lynn AM,Mishra S

    更新日期:2020-02-01 00:00:00

  • A pore creation in a triangular network model membrane.

    abstract::Membrane electroporation seems to be a useful method for delivery of biological active compounds into the cell. Although it is known that this phenomenon is sensitive to the electric field intensity, duration of the electric pulse and its shape, it is not fully understood. In some theoretical descriptions it is postul...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.02.001

    authors: Kubica K

    更新日期:2008-06-01 00:00:00

  • Detection of nucleotide sequences capable of forming non-canonical DNA structures: Application of automata theory.

    abstract::In this study, we develop a program that allows us to reveal DNA receptors, i.e. nucleotide sequences that may form more than one non-canonical structure. The data obtained may be analysed either experimentally or using DNA banks, and refers to the coding, non-coding or promotor region of the gene. These results provi...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.04.009

    authors: Yurushkin MV,Gervich LR,Bachurin SS,Kletskii ME

    更新日期:2019-06-01 00:00:00

  • Inhibitory activity of hibifolin on adenosine deaminase- experimental and molecular modeling study.

    abstract::Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflamm...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.08.005

    authors: Arun KG,Sharanya CS,Sandeep PM,Sadasivan C

    更新日期:2016-10-01 00:00:00

  • In silico study of porphyrin-anthraquinone hybrids as CDK2 inhibitor.

    abstract::Cyclin-Dependent Kinases (CDKs) are known to play crucial roles in controlling cell cycle progression of eukaryotic cell and inhibition of their activity has long been considered as potential strategy in anti-cancer drug research. In the present work, a series of porphyrin-anthraquinone hybrids bearing meso-substituen...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.12.005

    authors: Arba M,Ihsan S,Ramadhan OA,Tjahjono DH

    更新日期:2017-04-01 00:00:00