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Insights into Modeling Approaches in Chemistry: Assessing Ligand‐Protein Binding Thermodynamics Based on Rigid‐Flexible Model Molecules

Komarov, Igor V. ; Bugrov, Volodymyr A. ; Cherednychenko, Anton ; Grygorenko, Oleksandr O.

Chemical record, 2024-02, Vol.24 (2), p.e202300276-n/a [Periódico revisado por pares]

United States: Wiley Subscription Services, Inc

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  • Título:
    Insights into Modeling Approaches in Chemistry: Assessing Ligand‐Protein Binding Thermodynamics Based on Rigid‐Flexible Model Molecules
  • Autor: Komarov, Igor V. ; Bugrov, Volodymyr A. ; Cherednychenko, Anton ; Grygorenko, Oleksandr O.
  • Assuntos: Binding ; binding thermodynamics ; Chemistry ; conformationally flexible ; conformationally rigid ; Drug development ; Dynamic characteristics ; Enthalpy ; Entropy ; Free energy ; Ligands ; model compounds ; Modelling ; Protein Binding ; protein-ligand binding ; Proteins ; Proteins - chemistry ; Thermodynamics
  • É parte de: Chemical record, 2024-02, Vol.24 (2), p.e202300276-n/a
  • Notas: ObjectType-Article-2
    SourceType-Scholarly Journals-1
    ObjectType-Feature-3
    content type line 23
    ObjectType-Review-1
  • Descrição: In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein‐ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein‐ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein‐ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some “rules of thumb” have started to emerge on how to minimize entropy‐enthalpy compensation and design efficient rigidified or flexible ligands. Protein ligands exhibiting nearly identical composition and having equal numbers of functional groups while differing in molecular flexibility/rigidity are excellent model molecules to study the thermodynamics of the protein‐ligand binding. The design of the rigid/flexible ligands, methods of their investigation, and the results of systematic studies aiming at structural and dynamical features determining the binding thermodynamics are reviewed.
  • Editor: United States: Wiley Subscription Services, Inc
  • Idioma: Inglês
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