Abstract

Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted. In the work, we propose an approach to “smart design” of heterostructures (quantum wells and superlattices) based on the combination of Inverse Scattering Problem Method and the direct solution of the eigenvalue problem for the Schrödinger equation with reconstructed potentials. Potential shape reconstructed in this way can be substituted then by some approximation, so that the output spectrum obtained by solving the Schrödinger equation with such approximated potential, differs only slightly from the input one. In our opinion, the approach can be used in many applications, for instance, for developing the new electronic devices such as tunable THz detectors. Haemophilus influenzae type b (Hib) is one of the leading causes of invasive bacterial infection in young children. It is characterized by inflammation that is mainly mediated by cytokines and chemokines. One of the most abundant components of the Hib outer membrane is the P2 porin, which has been shown to induce the release of several inflammatory cytokines. A synthetic peptide corresponding to loop L7 of the porin activates JNK and p38 mitogen-activated protein kinase (MAPK) pathways. It has also been reported that a novel use of the complementary peptide approach to design a peptide that is able to bind selectively to the protein P2, thereby reducing its activity. In this in silico study we used of higher levels of our complement conserved structure ligand based binding pocket drug interactive theory to increase the accuracy of protein-ligand binding affinity predictions, resulting in better hit identification success rates as well as more efficient lead optimization processes. Here, we discovered for the first time the GENEA-Poriflunzaten-5567 a Peptide-mimic novel pharmacoelements complementary to the active loop of porin P2 from Haemophilus influenzae for the annotated modulation of its activity using Molecular simulation methods in arational in silico drug-target flexibility complement “Smart Design” methodology of Quantum Wells and Double-Quantum Wells Structures for the generation of a peptide-mimic novel pharmacoelement binding to the amino acid conserved sequences of the active loop of a Haemophilus influenzae porin P2.

Keywords

combined-applicationknowledge-basedpose-scoringphysical-forcefield-basedhit-scoringfunctions “Smart Design” of Quantum Wells and Double-Quantum Wells Structures A rational in silico drug-target flexibility complement methodology-design for the generation of a peptide-mimic novel pharmacoelement binding to the amino acid conserved sequences of the active loop of a Haemophilus influenzae porin P2, biomolecular simulation, molecular modelling, molecular dynamics, force fields, quantum mechanics/molecular mechanics, quantum chemical modelling