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The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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A neutral atom consists of a positively charged nucleus surrounded by a negatively charged electron cloud. When placed in an external electric field, the external electric force pulls the electrons and nucleus apart, opposite to the intrinsic attraction between the nucleus and the electrons. The opposing forces balance each other with a slight shift between the center of masses of the nucleus and the electron cloud, resulting in a polarized atom. On the other hand, a few molecules, like water,...
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Updated: Aug 19, 2025

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Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force

Grzegorz Nawrocki1, Igor Leontyev1, Serzhan Sakipov1

  • 1InterX Inc., 805 Allston Way, Berkeley California, 94710, United States.

Journal of Chemical Theory and Computation
|December 2, 2022
PubMed
Summary
This summary is machine-generated.

The ARROW force field, a physics-based model, accurately predicts protein-ligand binding free energies. This advancement in molecular dynamics simulations aids in in silico drug design.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics Simulations
  • Drug Design

Background:

  • Molecular dynamics (MD) simulations are crucial for in silico drug design.
  • Accurate force fields (FFs) are essential for reliable binding free-energy calculations.
  • Existing FFs may struggle with complex protein-ligand interactions.

Purpose of the Study:

  • To evaluate the ARROW force field for protein-ligand binding free-energy calculations.
  • To extend the ARROW FF parameterization to include all amino acids and charged groups.
  • To assess the accuracy of ARROW FF predictions compared to established methods.

Main Methods:

  • Utilized the ARROW force field, a multipolar polarizable and physics-based model.
  • Extended ARROW FF parameters using high-level ab initio quantum mechanical (QM) calculations.
  • Employed a novel Hamiltonian Replica exchange (HREX) technique coupled with potential softening and nonequilibrium MD for adequate sampling.

Main Results:

  • ARROW FF achieved near chemical accuracy (∼0.5 kcal/mol MAE) for MCL1 and Thrombin systems.
  • The ARROW FF demonstrated comparable accuracy to leading nonpolarizable FFs for the studied protein systems.
  • Accurate prediction of dimer interaction energies involving polar and charged species remains a challenge (CDK2 system).

Conclusions:

  • The ARROW force field shows significant promise for accurate protein-ligand binding free-energy predictions.
  • The extended ARROW FF is suitable for molecular simulations of protein-ligand systems.
  • Further development may be needed to address challenges with polar and charged interactions in specific systems.