Background:
Protein-protein interactions (PPIs) are becoming increasingly important as PPIs
form the basis of multiple aggregation-related diseases such as cancer, Creutzfeldt-Jakob, and Alzheimer’s
diseases. This mini-review presents hybrid quantum molecular dynamics, quantum chemical,
topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these
theoretical studies facilitate the discovery of some PPI inhibitors of therapeutic importance.
Objective:
The objective of this review is to present hybrid quantum molecular dynamics, quantum
chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show
how these theoretical studies enable the discovery of some PPI inhibitors of therapeutic importance.
Methods:
This article presents a detailed survey of hybrid quantum dynamics that combines classical
and quantum MD for PPIs. The article also surveys various developments pertinent to topological, graph
theoretical, group theoretical and docking studies of PPIs and highlight how the methods facilitate the
discovery of some PPI inhibitors of therapeutic importance.
Results:
It is shown that it is important to include higher-level quantum chemical computations for accurate
computations of free energies and electrostatics of PPIs and Drugs with PPIs, and thus techniques
that combine classical MD tools with quantum MD are preferred choices. Topological, graph theoretical
and group theoretical techniques are shown to be important in studying large network of PPIs comprised
of over 100,000 proteins where quantum chemical and other techniques are not feasible. Hence, multiple
techniques are needed for PPIs.
Conclusion:
Drug discovery and our understanding of complex PPIs require multifaceted techniques
that involve several disciplines such as quantum chemistry, topology, graph theory, knot theory and
group theory, thus demonstrating a compelling need for a multi-disciplinary approach to the problem.
Ultrarelativistic quantum molecular dynamics calculations of two-pion Hanbury-Brown–Twiss correlations in central Pb-Pb collisions atsNN=2.76TeV