In silico analysis suggests interaction between Ebola virus and the extracellular matrix

Veljković, Veljko; Glišić, Sanja; Scotch, Matthew; Branch, Donald R.; Perovic, Vladimir; Senćanski, Milan; Veljković, Nevena; Colombatti, Alfonso

doi:10.3389/fmicb.2015.00135

Cited by 27 publications

(31 citation statements)

References 58 publications

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“…ISM procedure has been detailed [3][4][5][6][23][24][25]. A summary of ISM procedure engaged in these studies is provided in section 2.1.…”

Section: Methodsmentioning

confidence: 99%

“…This has been defined as energy in terms of valence electrons [3-6, 13, 23-25]. In case of bio-molecules including the molecules of pharmacological agents and their molecular targets such as proteins and peptides or genes and proteins encoding them, their EIIP values have preliminarily been determined [3][4][5][6] using the equation obtained from the General Model Pseudo-Potential [3][4][5][6] and shown below. EIIP rules the first interaction (Inter-molecular) and engages the three following processes:…”

Section: Inter-molecular Interactionsmentioning

confidence: 99%

“…This is because computational approaches are resource and time saving as they are not labor-intensive [1,2]. Such computational approaches include the Digital Signal Processing (DSP)-based Bioinformatics procedures like Informational Spectrum Method (ISM) [3][4][5] and Resonant Recognition Method (RRM) [6].…”

Section: Introductionmentioning

confidence: 99%

“…Other antiretroviral agent studied using ISM and a biological parameter includes Maturation Inhibitors (Bevirimat (BVM)). In this case, EIIP was utilized [3][4][5][6]10]. Integrase Enzyme Inhibitors (Raltegravir ) was examined by means of LIFS790103 [5,6,10].…”

Section: Introductionmentioning

confidence: 99%

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Novel Computerized Approaches to Investigating Pharmacological Activities

Nwankwo¹

2015

CBB

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Abstract:Complementing clinical assessments using computerized procedures with the view of completely disengaging from clinical procedures may become inevitable in future. Huge biological and pharmacological data (such as sequences) are churned out daily such that it is becoming difficult to process them without the aid of computers. Computerized approaches including Digital Signal Processing (DSP)-based Bioinformatics procedures like Informational Spectrum Method (ISM) are rational techniques that need be incorporated into pharmacological studies. By means of ISM and one biological parameter or Amino Acid Scale (AAS), we have preliminarily shown how pharmacological activities can be decoded using computerized techniques. However, for effective engagement of ISM, some basic information must be made available and engaged. Firstly, the sequence information comprising of the consensus sequences and all the mutations involved must be assembled and engaged. Pharmacological activities (e.g. drug resistance) are known to be expressed in the genes/proteins (e.g. MDR1 and MDR2, pfdr1, etc). Secondly, biological parameters must be identified and engaged. This calls for good knowledge of the drugs' mechanisms of action at the atomic level. This is because it has been identified that, at one point mutation; more than one biological parameter may be involved. To obtain the entirety of pharmacological activities exhibited therefore, aggregation of the contributions from each mutation and parameter is needed.We have then unveiled and compared the pharmacological activities of anti-retroviral agents (Enfuvirtide and Sifuvirtide), and potencies of Malaria vaccine candidates, peptides P18 and P32 (Innocentive Challenge Winning Solver Award, ID: 9933477), etc. A biomedical device called Computer-Aided Drug Resistance Calculator (Patent Application filed in 2014) is developed using this novel computerized approach. The device will rationally help assess a pharmacological property (drug resistance). Other researchers have recorded in-silico pharmacological assessments. Clinically and computationally derived outcomes are found to correlate. We therefore propose that these computerized approaches be engaged in deciphering pharmacological activities where sequence information and biological parameters are available. These approaches are rational. They also present pharmacological findings in numerical terms. In this era of rational, computerized, informatics-and robotics-based procedures, these approaches are envisaged to transform pharmacological investigation procedures especially now that pharmacological activities could be deciphered from their protein sequences or those of their protein targets and the genes/proteins expressing them. The procedures engaged in this study are expected to be embodied into Pharmaco-informatics program.

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“…ISM procedure has been detailed [3][4][5][6][23][24][25]. A summary of ISM procedure engaged in these studies is provided in section 2.1.…”

Section: Methodsmentioning

confidence: 99%

Section: Inter-molecular Interactionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Novel Computerized Approaches to Investigating Pharmacological Activities

Nwankwo¹

2015

CBB

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“…75 In another study, EBOV-human PPIs were investigated through in silico virtual spectroscopy (informational spectrum method) method to decipher key interactions of EBOV glycoprotein and host endothelial extracellular matrix. 76 Although far from complete and still in a developmental flux, huge primary databases of intraviral and virus-host PPIs have been built so far, such as in VirHostNet and VirusMINT. 77,78 In combination with literature-derived lowthroughput interaction data, Meyniel-Schicklin et al have used these high-quality curated PPI datasets in an integrative and comparative computational analysis of all intraviral and virus-human interactomes through the implementation of graph theory and other computational modelings.…”

mentioning

confidence: 99%

Recent advances in host–virus interactomics during entry and infection

Bhattacharjee¹

2015

VAAT

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Viral infections and pandemics result in millions of deaths worldwide each year. Viruses exploit host cellular processes, not only to gain entry and to deliver their genetic cargo, but also to counteract and use host immune defenses. To this end, a variety of ingenious strategies have evolved in viruses that involve fusion between virus and host membranes, channel formation through the host plasma membranes, disruption of the membrane vesicles, or a combination of these events. The entry and infection pathways of virus are thus largely defined by the interactions between virus particles and their cell surface and cytoplasmic receptors. A thorough analysis of virus-host interactomes may reveal novel mechanisms in virus entry, virus infection, and pathogenic strategies to modulate host metabolic pathways. The study of viral entry, infection, and pathogenesis has evolved over a long period. A host of next-generation technological advancements in this field has been discussed in this review.

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