Forthcoming and Online First Articles

International Journal of Computational Biology and Drug Design

International Journal of Computational Biology and Drug Design (IJCBDD)

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International Journal of Computational Biology and Drug Design (7 papers in press)

Regular Issues

  • Importance of safety maintenance of the survived with recent former infection experience during a pandemic syndrome episode: A Study by Difference Equation Approach   Order a copy of this article
    by Subhasis Bhattacharya, Suman Paul, Sudip Mukherjee 
    Abstract: During the outbreak of a highly infectious disease conceded by a virus, handling of healthcare catastrophe is the most momentous part. Any type of known or unknown relaxation may generate enormous loss in terms of population. Present study consider the concern that survived one who has some fresh former infection history can be fingered with appropriate care throughout the syndrome period otherwise a huge harm can be advent by the state. The study follow difference equation modelling considering two aspects where the survived with former infection history handled with care and not reckoned as a part of sustained population and the other is they encompassed with the general population category. The study considers an example of a hypothetical state with some give infection rate, death rate and quarantine rate. By using R- programme language the study observes that proper care for such group of population is very significant to reduce the situation like human loss.
    Keywords: Infectious disease; SARS-CoV-2; 2019-nCov; Difference Equation; Survived from the infected; Quarantine rate; Death Rate.

  • A Geometry based Approach to Compare Five Metal Binding Sites on Biomolecular Structures   Order a copy of this article
    by Swati Adhikari, Parthajit Roy 
    Abstract: Characterization of type or function of a coordination site on the structure of biomolecules protein, DNA and RNA is a very critical task. Sometimes it is needed to compare a new site with an existing one, to predict structural properties or function of the new site and to compute various coordination statistics. Now, different coordination sites possess different geometries. So, the task is to compare an unknown site with a known one possessing the same geometries and to compute statistics regarding structural deviations. For the same purpose, in this study, three novel algorithms have been proposed that use a geometry-based concept to compare five pairs of coordination sites. To produce minimum mean square error (MSE) due to the structural deviations, some mathematical transformations have been applied on each pair of structures to make them structurally compatible. Bio-researchers get benefitted from the numerous statistical reports obtained with these algorithms.
    Keywords: Biomolecule-Metal Interaction; Coordination Site; Coordination Geometry; Algorithms in Bioinformatics.

  • Molecular Docking of an antianxiety drugs molecule 3-[2-(1H-Benzimidazol-2-ylsulfan-yl) eth-yl]-1,3-oxazolidin-2-one   Order a copy of this article
    by Abdellatif BOUAYYADI, Aissam EL ALIANI, Yassine KASMI, Ahmed MOUSSAIF, Abdelhalim MESFIOUI, El Mokhtar ESSASSI, Mohamed EL MZIBRI 
    Abstract: The "3-[2- (1H-Benzimidazol-2-ylsulfan-yl) eth-yl] -1,3-oxazolidin-2-one "(OXB1), a newly synthesised and characterised molecule from the family of Benzimidazole, represents a class of molecules with potential anxiolytic activity. In this work we have evaluated, in silico, the binding capacity of this molecule to the active site of gamma-aminobutyric acid (GABA) located in the GABA type A receptor (GABAAR). Results showed a similar affinity to the 3 main isoforms of the GABAAR subtypes: ?2?2?2, ?3?2?2 and ?5?2?2 with respectively 7.3, 7.0 and 7.2. Molecular dynamic explorations showed a high stability of the complex (OXB1-GABAAR). Moreover, the evaluation of the ADMET profile of OXB1 clearly showed that this chemical exhibits good pharmacokinetics and pharmacodynamics properties and is able to cross the blood brain barrier to reach the potential targets in the brain, suggesting that this molecule could be an effective and potential anxiolytic agent that could be used for in vivo explorations to strengthen the therapeutic arsenal against anxiety with more efficacy and less side effects.
    Keywords: Benzemidazole; GABA; GABAA receptor; GABA Agonist; Anxiety.

  • An Optimal Procedure Using Six Mathematical Models to Control Tribolium casta-neum Exposed to Some Essential Plant Oils   Order a copy of this article
    by Elhadi Elamir 
    Abstract: The present study employs six models and consequently an optimal procedure, to develop a powerful strategy to manage Tribolium castaneum insects exposed to different concentrations of essential oils extracted from four plants. These models are composed of three kinds of logistic models i.e. Logit, Loglog and Cloglog models, together with Probit, Cauchit and Fractional models. The author uses a generalized inverse matrix method to find the least-squares solution of the obtained regular matrix equations. The results of this research assure that the proposed optimal procedure, Probit model, Logit model and CLoglog model may control the mortality of Tribolium castaneum with accepted goodness of fit. Results of this research can be used to determine the oil concentrations corresponding with the mortality ratios of the insects which can be used to build an integrated and precise control system to compact Tribolium castaneum insects.
    Keywords: Probit; Logistic; Cauchit; Fractional models; T. castaneum.

  • EXPLORING THE FUNCTIONS AND INTERACTIONS OF UNDECIPHERED PROTEINS FROM SHIGELLA FLEXNERI   Order a copy of this article
    by Sarmishta Mukhopadhyay, Sayak Ganguli, SANTANU CHAKRABARTI 
    Abstract: Multiple serotypes of Shigella and surfacing of antimicrobial resistant strains pose a serious threat in treating shigellosis. A significant proportion of the Shigella flexneri genome (18%) codes for Hypothetical Proteins (HPs), which may be involved in key cellular and signaling pathways, that play decisive role in pathogen survival and dissemination. This work employs a computational workflow to determine the family, domain, sub-cellular localization and possible interacting partners of these unannotated proteins. The investigation could successfully assign functions to 432 HPs from Shigella flexneri genome and classified them into 20 different groups in accordance with their functions. Enzymes being the most prevalent group, were further categorized into several classes depending on the reaction it catalyzes. This work should serve as a reference pipeline for annotation of other HPs from pathogenic organisms and detailed experimental investigations of these annotated proteins should help us to identify novel therapeutic targets for future drug discovery.
    Keywords: Shigella sp; Shigellosis; Hypothetical Proteins; In-silico; Therapeutic Targets.

  • Generation of 2D-QSAR and pharmacophore models for fishing better anti-leishmanial therapeutics   Order a copy of this article
    by Clayton Fernando Rencilin, Joseph Christina Rosy, Krishnan Sundar 
    Abstract: Leishmaniasis, a life-threatening tropical disease, is caused by 20 different species of Leishmania parasites. The disease, that is endemic in nearly 100 countries, contributes to millions of deaths each year. However, very few anti-leishmanial compounds are available in the market and that too possess many drawbacks. Hence, the therapeutic arsenal requires potential and novel anti-leishmanial compounds to treat Leishmaniasis. In the present study, Quantitative Structure Activity Relationship (QSAR) model and Pharmacophore model were developed with a set of anti-leishmanial compounds collected from literature and commercial anti-leishmanial drugs. Novel compounds matching the Pharmacophore was screened which can be potentially be used to treat Leishmaniasis. The compounds were segregated into training and test sets and, QSAR models were developed by Multiple Linear Regression (MLR) method using EasyQSAR. Further, pharmacophore model was derived by physio-chemical features of the selected compounds using PharmaGist. Using MLR, different QSAR models were developed using various molecular descriptors. Further, the percentage contribution of descriptors on each model was studied. The models were validated using the test sets with statistical measures. A ligand-based pharmacophore model was developed using active compound as template. The pharmacophore model was used for searching the purchasable compound dataset of ZINC database for matching compounds. The theoretical activities, ADME and drug likeness properties of top compounds were analyzed. Thirteen novel, readily purchasable compounds were obtained from this approach, which shows good predicted activity, ADME and druglikeness. These compounds can be regarded as potential candidates to be developed as novel anti-leishmanial drugs with improved activity and reduced side effects.
    Keywords: Antileishmanial compounds; descriptor; pharmacophore; ZINCPharmar; Pharmacophore search and QSAR.

  • Computational Approach against Dengue Virus Type 2 Nonstructural Protein (NS1) form using Hepatoprotective Plant Secondary Metabolites   Order a copy of this article
    by Krishn Kumar Agrawal, Yogesh Murti 
    Abstract: Background: Dengue virus (DENV) causes dengue fever, dengue hemorrhagic illness, and dengue shock syndrome. Objective: This investigation was intended to evaluate secondary metabolites of hepatoprotective plant against DENV type 2 nonstructural protein (NS1) formutilizing a molecular docking method. Methodology: The three dimensional structure ofDENV NS1form was fetched from the protein data bank. The ligands structure were fetched from the Pubchem data base in sdf format and converted in to mol2 format using OpenBabel. Finally the docking was performed by using iGEMDOCK software tool. Result & Discussion: The binding energy of kaempferol-3-O-rutinoside, lithospermic acid, hesperidin and rutin were found to be -108.73, -108.59, -103.72, and -102.5 kcal/mol respectively. Conclusion: On the basis of result of the present research, DENV protein inhibitors may now be identified by using this knowledge, and some have already been identified. Clinical trials are being conducted to verify the result of in-silico studies.
    Keywords: Dengue virus; kaempferol-3-O-rutinoside; NS1; computational approach; in-silico.