Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework

Electrostatic interactions between biological molecules are crucially influenced by their aqueous environment, with efficient and accurate models of solvent effects required for robust molecular design strategies. Continuum electrostatic models provide a reasonable balance between computational efficiency and accurate system representation. In this article, I review two specific molecular design strategies, charge optimization and combinatorial design, paying particular attention to how the continuum framework (also briefly described herein) successfully enables both theoretical insights and molecular designs and presents a challenge in design applications due to what I call “the isostericity constraint.” Efforts to work around the isostericity constraint and other challenges are discussed. Additionally, particular emphasis is placed on using such models in the rational design of particularly tight, specific, or promiscuous interactions, in keeping with the increased sophistication of current molecular design applications.