With the advancement of “proteomics” data and systems biology, new techniques are needed
to meet the new era of drug discovery. Network theory is increasingly applied to describe complex biological
systems, thus implying its essential roles in system-based drug design. In this review, we first
summarized general network parameters used in describing biological systems, and then gave some
recent applications of these network parameters as topological indices in drug design in terms of Protein
Structure Networks (PSNs), Protein-Protein Interaction Networks (PPINs) including related structural
PPINs, and Elastic Network Models (ENMs). These network models have enabled the development of
new drugs relying on allosteric effects, describing anti-cancer targets, targeting hot spots and key proteins
at the protein-protein interfaces and PPINs, and helped drug design by modulating conformational
flexibility. Accordingly, we highlighted the integration of network models bringing new paradigms into
the next-generation target-based drug discovery.
Keywords: Allosteric drugs, Biological networks, Drug targets, Hot spots, structural PPINs, Target flexibility.
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