ijms-logo

Journal Browser

Journal Browser

Computational Eco, Bio, and Pharmaco-Toxicity 2016

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Toxicology".

Deadline for manuscript submissions: closed (31 December 2016) | Viewed by 13189

Special Issue Editor


E-Mail Website
Guest Editor
1. Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi 16, 300115 Timisoara, Romania
2. Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter–INCEMC–Timisoara, Str. Dr. Aurel Podeanu 144, 300569 Timișoara, Romania
Interests: quantum physical chemistry; nanochemistry; reactivity indices and principles; electronegativity; density functional theory; path integrals; enzyme kinetics; QSAR; epistemology and philosophy of science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last few decades, world scientific research has been focused on so-called green chemistry, which consists in efforts to reduce or eliminate the use or production of dangerous substances (with toxic potential) in synthesis, mainstream usage and application of chemical compounds through pre-industrial or computational design. As such, on all meridians, national and international organizations advanced laws for the validation of chemical compounds entering the environment, and economical and medicinal cycles: The first taxonomical groups emerged in United States from the Environmental Protection Agency (EPA, 1991), followed by the European agency, Umweltbundesamt (1997), and by Environment Canada (1999). However, at the level of the European Union, since the program of Strategy on Management of Substances (SOMS, 2001), the next step was made by the European Commission on 23 October, 2003, then by the directive EC no. 1907/2006 and, finally by setting the Registration, Evaluation, Authorization and Restriction of Chemicals (REACH) norms according which, from 2009, any substance with carcinomic or mutagenic potential will step into the eco–bio–pharma life-cycle and economical market only with authorization from the European Chemical Agency (ECMA) in Helsinki.

In this context, fundamental research is at a turn, driven by the international and EU resolutions, through the directives of the Organization of Economical and Cooperation Development (OECD); for instance, the quantitative structure-activity relationship (QSAR) methodology is currently credited as the only and certain source of computational design for tested compounds with bio-, eco-, and pharmaco-logical impacts (OECD, 2004).

Overall, the present editorial endeavor provides an input for future enterprises of intense conceptual–computational and experimental research, aimed at profoundly studying the particular systems involved in the bio-, eco-, and pharmaco-logical actions, e.g., supra-molecules, enzymes/ligands structures and action, ionic liquids, antagonists, and inhibitors, to name a few. You are kindly invited to contribute to such a worthy future.

Dr.-Habil. PI Mihai V. Putz
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Acetylcholinesterase
  • Anionic-cationic interaction
  • Biodegradability
  • Correlation map
  • Cyclohexylamine
  • Cytotoxicity
  • Daphnia magna
  • Ecotoxicological principles
  • Ecotoxicology
  • Electric eel
  • Endoplasmatic reticulum
  • Ergodic
  • ESIP (Element Specific Influence Parameter) Köln model
  • Flavonoids
  • Gram-Schmidt algorithm
  • Hansch factors
  • Hydrolysis velocity
  • Hydrophobicity
  • Ionic liquid modeling
  • Lipophylicity
  • Metabolism
  • Microorganisms
  • Multicolinearity
  • Naringenin
  • Polarizability
  • Proton-pump inhibitors
  • QSAR approaches/equations
  • QSAR equation
  • Spectral paths
  • SPECTRAL-SAR algorithm
  • Steric effects
  • Topliss-Costello rule

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

5037 KiB  
Article
Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase
by Beata Szefler, Mircea V. Diudea, Mihai V. Putz and Ireneusz P. Grudzinski
Int. J. Mol. Sci. 2016, 17(11), 1796; https://doi.org/10.3390/ijms17111796 - 27 Oct 2016
Cited by 10 | Viewed by 6230
Abstract
Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously [...] Read more.
Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of −5.8 kcal/mol and (LIG2) of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase. Full article
(This article belongs to the Special Issue Computational Eco, Bio, and Pharmaco-Toxicity 2016)
Show Figures

Graphical abstract

Review

Jump to: Research

3146 KiB  
Review
Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions
by Mihai V. Putz, Corina Duda-Seiman, Daniel Duda-Seiman, Ana-Maria Putz, Iulia Alexandrescu, Maria Mernea and Speranta Avram
Int. J. Mol. Sci. 2016, 17(7), 1087; https://doi.org/10.3390/ijms17071087 - 08 Jul 2016
Cited by 27 | Viewed by 6217
Abstract
Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the [...] Read more.
Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. Full article
(This article belongs to the Special Issue Computational Eco, Bio, and Pharmaco-Toxicity 2016)
Show Figures

Graphical abstract

Back to TopTop