Computational design of phage cocktails based on phage-bacteria infection networks

Background: In view of many current mosquito-borne diseases there is a need for the design of novel repellents. Objective: The objective of this article is to review the results of the researches carried out by the authors in the computer-assisted design of novel mosquito repellents. Methods: Two methods in the computational design of repellents have been discussed: a) Quantitative Structure Activity Relationship (QSAR) studies from a set of repellents structurally related to DEET using computed mathematical descriptors, and b) Pharmacophore based modeling for design and discovery of novel repellent compounds including virtual screening of compound databases and synthesis of novel analogues. Results: Effective QSARs could be developed using mathematical structural descriptors. The pharmacophore based method is an effective tool for the discovery of new repellent molecules. Conclusion: Results reviewed in this article show that both QSAR and pharmacophore based methods can be used to design novel repellent molecules.

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Molecular Design of Peptide-Fc Fusion Drugs

Current Drug Metabolism ◽

10.2174/1389200219666180821095355 ◽

2019 ◽

Vol 20 (3) ◽

pp. 203-208 ◽

Cited By ~ 3

Author(s):

Lin Ning ◽

Bifang He ◽

Peng Zhou ◽

Ratmir Derda ◽

Jian Huang

Keyword(s):

Rational Design ◽

Molecular Design ◽

Computational Design ◽

Fusion Technology ◽

Computational Tools ◽

Open Questions ◽

Biological Therapeutics ◽

Key Steps ◽

Computational Resources ◽

Tools And Methods

Background:Peptide-Fc fusion drugs, also known as peptibodies, are a category of biological therapeutics in which the Fc region of an antibody is genetically fused to a peptide of interest. However, to develop such kind of drugs is laborious and expensive. Rational design is urgently needed.Methods:We summarized the key steps in peptide-Fc fusion technology and stressed the main computational resources, tools, and methods that had been used in the rational design of peptide-Fc fusion drugs. We also raised open questions about the computer-aided molecular design of peptide-Fc.Results:The design of peptibody consists of four steps. First, identify peptide leads from native ligands, biopanning, and computational design or prediction. Second, select the proper Fc region from different classes or subclasses of immunoglobulin. Third, fuse the peptide leads and Fc together properly. At last, evaluate the immunogenicity of the constructs. At each step, there are quite a few useful resources and computational tools.Conclusion:Reviewing the molecular design of peptibody will certainly help make the transition from peptide leads to drugs on the market quicker and cheaper.

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Computational Design of Centralized HIV-1 Genes

Current HIV Research ◽

10.2174/157016210794088263 ◽

2010 ◽

Vol 8 (8) ◽

pp. 613-621 ◽

Cited By ~ 17

Author(s):

Miguel Arenas ◽

David Posada

Keyword(s):

Computational Design ◽

Hiv 1

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Quantitative structure-activity relationship model, molecular docking simulation and computational design of some novel compounds against DNA gyrase receptor.

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200625142447 ◽

2020 ◽

Vol 16 ◽

Author(s):

Shola Elijah Adeniji

Keyword(s):

Biological Activity ◽

Molecular Docking ◽

Binding Energy ◽

Biological Activities ◽

Docking Simulation ◽

Dna Gyrase ◽

Computational Design ◽

Multi Drug Resistance ◽

Drug Candidate ◽

Standard Drug

Introduction: Mycobacterium tuberculosis has instigated a serious challenge toward the effective treatment of tuberculosis. The reoccurrence of the resistant strains of the disease to accessible drugs/medications has mandate for the development of more effective anti-tubercular agents with efficient activities. Time expended and costs in discovering and synthesizing new hypothetical drugs with improved biological activity have been a major challenge toward the treatment of multi-drug resistance strain M. tuberculosis (TB). Meanwhile, to solve the problem stated, a new approach i.e. QSAR which establish connection between novel drugs with a better biological against M. tuberculosis is adopted. Methods: The anti-tubercular model established in this study to forecast the biological activities of some anti-tubercular compounds selected and to design new hypothetical drugs is subjective to the molecular descriptors; MATS7s, SM1_DzZ, SpMin4_Bhv, TDB3v and RDF70v. Ligand-receptor interactions between quinoline derivatives and the receptor (DNA gyrase) was carried out using molecular docking technique by employing the PyRx virtual screening software and discovery studio visualizer software. Furthermore, docking study indicates that compounds 20 of the derivatives with promising biological activity have the utmost binding energy of -17.79 kcal/mol. Results: Meanwhile, the interaction of the standard drug; isoniazid with the target enzyme was observed with the binding energy -14.6 kcal/mol which was significantly lesser than the binding energy of the ligand (compound 20).Therefore, compound 20 served as a template structure to designed compounds with more efficient activities. Among the compounds designed; compounds 20p was observed with better anti-tubercular activities with more prominent binding affinities of -24.3kcal/mol. Conclusion: The presumption of this research aid the medicinal chemists and pharmacist to design and synthesis a novel drug candidate against the tuberculosis. Moreover, in-vitro and in-vivo test could be carried out to validate the computational results.

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