In silico screening of plant peptides against the envelope protein of dengue virus

@#Peptide therapeutics are found to be an emerging and attractive class of treatment due to their highly specific and safe nature. Hence twenty plant peptides were subjected to screening by molecular docking against the envelope protein of the dengue virus using Clus Pro, Patch Dock, and HADDOCK servers. Physicochemical parameters, allergenicity, and toxicity profile of the plant peptides were estimated by Protparam analysis, AllergenFP, and ToxinPred web servers. Six potential compounds namely Ginkbilobin, Cycloviolin-D, Circulin-B, Circulin-A, Cycloviolacin-013, and Circulin-C showed the highest binding energy with both nonallergenic and nontoxic properties. They also exhibited desirable half-lives extending to 30 hrs except for Ginkbilobin, which showed the least half-life of 4.4 hours and non-polar activity. The residues of Ala-4 of Ginkbilobin; Arg-30 of Cycloviolin D; Arg-29 of Circulin A and C interacted with the Try 101 of the domain II of Envelope protein, implying the possible inhibition of the insertion process of the trimeric E protein during fusion with the host cells. Thus, the identified plant peptides could serve as potential leads upon further subjection to in vitro studies.

Estudio y análisis comparativo de interacciones entre la proteina integrina con fragmentos de la proteína fibrilina-1 y fragmentos mutados de esta utilizando la metodología de docking molecular / Study and comparative analysis of interactions protein between the integrina with fragments fibrillin-1 and mutated fragments of this by using molecular docking

Resumen Objetivo: Evaluar las interacciones proteína-proteína que pueden generarse entre fragmentos de la proteína fibrilina-1, cuyas mutaciones causan el síndrome de Marfan (SM). Materiales y métodos: Se realizó una serie de cálculos docking proteína-proteína entre las macromoléculas de interés; se empleó el programa Molsoft ICM; se utilizaron las estructuras cristalinas de la proteína integrina αVβ3 y los fragmentos de la proteína fibrilina-1; además se generó una sucesión de mutaciones en la fibrilina-1, las cuales son características de pacientes con síndrome de Marfan, y posteriormente se realizó el acoplamiento molecular. Adicionalmente se determinó los aminoácidos que con mayor frecuencia estaban presentes en el sitio de interacción y su hidrofobicidad. Resultados: Se cuantificó la cantidad de aminoácidos hidrófobos presentes en las zonas de interacción producidas por los acoplamientos, teniendo en cuenta la energía del sistema; esta ponderación estuvo entre el 40 y 50 % de los aminoácidos de la zona de interacción, con un porcentaje mayor con respecto a aminoácidos neutros o cargados. En los resultados obtenidos utilizando las mutaciones realizadas sobre los fragmentos cbEGF22-TB4-cbEGF23 y cbEGF9-hyb2-cbEGF10 de la fibrilina-1 se encontró que no se ubicaron en zonas cercanas al sitio de interacción en la mayoría de los casos. Conclusiones: Las interacciones entre los fragmentos de fibrilina-1, y estos con respecto a la integrina, mostraron en sus zonas de interacción la presencia mayoritariamente de aminoácidos hidrofóbicos, que es lo esperado normalmente.

Abstract Objective: To assess protein-protein interactions between fragments of fibrillin-1 protein, whose mutations cause Marfan syndrome (MS). Materials and Methods: We performed a series of protein-protein docking calculations between the macromolecules of interest for this purpose was used Molsoft ICM program. We used the crystal structures of αVβ3 Integrin protein and fragments of fibrillin-1 protein also were generated mutations in the fibrillin-1, which are characteristic in patients with Marfan syndrome and subsequently to the molecular docking. We determined the amino acids most often present at the site of interaction and its hydrophobicity. Results: The amount of hydrophobic amino acids present in the areas of interaction given by the couplings was quantified. Given the energy of the system, was between 40 and 50% of the amino acids of the interaction zone, with a higher proportion relative to charged or neutral amino acids. In the results obtained using the mutations performed on fragments cbEGF23 cbEGF22-TB4-and-cbEGF10 cbEGF9-HYB2 of fibrillin-1, was found they were not placed in areas near the site of interaction in most cases. Conclusion: The interaction between fragments of fibrillin-1, and those with respect to their integrin showed the presence interaction zones mostly hydrophobic amino acids, which are normally expected.

What in silico molecular docking can do for the ‘bench-working biologists’.

Required by an increasing amount of scientists, the in silico docking field is in full expansion, new algorithms and methods appearing at an exponential rate. The sheer range of available programs is overwhelming for the benchworking biologist, which is often discouraging by the lack of a graphical user interface, good user manual or literature to validate a given program. This mini-review attempts to present the docking problem and available solutions from a non-bioinformatician point of view and makes a selection of the available servers and programs. These tools are evaluated from several points of view, as numbers of citations, ease of usage and computer requirements. Finally, the capabilities and limitations as well as specific applications of in silico docking techniques are presented.

Progress in Protein-protein Docking Approaches / 生物化学与生物物理进展

Protein-protein interactions and recognition are the focal and hot themes of the life science field in the 21st century. Molecular docking approach is the effective computer modeling technology in the study of this topic. Generally, the protein-protein docking procedure is composed of four stages: searching of the binding modes of the receptor and the ligand, filtering of docked modes to eliminate the irrational docked structures, optimizing the structures, evaluating the docked modes with the refined scoring function and ranking them to obtain the near-native structures. Combining the research group's works, in terms of the international and national progress of protein-protein docking approaches, the detailed review was made about the four stages mentioned above. Additionally, the existing major questions are analyzed and the prospects of the future study are made.