In silico дослідження взаємодії гетероциклічних основ з пептидними групами білків: пофрагментний підхід

• Дата: 2021
• Автори: Velihina, Yevheniia S., Obernikhina, Nataliya V., Pilyo, Stepan G., Kachaeva, Maryna V., Kachkovsky, Oleksiy D.
• Формат: Стаття
• Мова: English
• Опубліковано: V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine 2021
• Теми: fragment-to-fragment approach; peptide bond; biological affinity; [Pharm-BioM] complex; п-stacking interaction; hydrogen bonding; підхід «фрагмент до фрагмента»; пептидні зв’язки; афінність зв’язування; комплекс [Фармакофор-Біомолекула]; п-стекінгова взаємодія; водневі зв’язки
• Онлайн доступ: https://bioorganica.com.ua/index.php/journal/article/view/46
• Назва журналу: Ukrainica Bioorganica Acta

The binding affinity of model peptide moieties (Pept) and heterocyclic bases involving 1,3-oxazoles that are condensed with pyridine and pyrimidine as pharmacophores (Pharm) was investigated in silico and analyzed within the “fragment-to-fragment” approach. The anellation of the heterocyclic rings increasing their acceptor properties is accompanied by gaining stability of the [Pharm-Pept] complexes formed by the p-stack interaction. It was found that elongation of the polypeptide chain led to a twofold increase of the stabilization energy of the [Pharm-Pept] complexes. The stability of the hydrogen bonding ([HB]) [Pharm-BioM] complexes formed by means of the interaction between the dicoordinated nitrogen atom of the heterocycle and the functional groups of peptide amino acids (-OH, -NH2, -SH) was evaluated. It was demonstrated that [HB]-complexes that were formed by hydrogen bonds formation with amino acid that contained OH groups had the largest stabilization effect. The anellation with pyridine and pyrimidine rings led to stability increase of the complexes formed by the hydrogen bonding mechanism. The binding energy of [HB]-complexes for compounds 2b and 3 with a "free" peptide bond of the extended part of the protein is lower compared to amino acids with OH-functional groups. On the contrary, the binding energy of compound 4 with peptides was 2 kcal/mol higher. Compound 4 demonstrated the most pronounced biological activity in vitro studies.