title: ÐÐ¾Ð¸ÑÐº Ð²Ð¾Ð·Ð¼Ð¾Ð¶Ð½ÑÑ Ð¸Ð½Ð³Ð¸Ð±Ð¸ÑÐ¾ÑÐ¾Ð² Ð´Ð»Ñ Ð±ÐµÐ»ÐºÐ¾Ð² SARS-CoV-2 Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð²Ð¸ÑÑÑÐ°Ð»ÑÐ½Ð¾Ð³Ð¾ ÑÐºÑÐ¸Ð½Ð¸Ð½Ð³Ð° Ð»Ð¸Ð³Ð°Ð½Ð´Ð¾Ð²
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Search for inhibitors for SARS-CoV-2 proteins using virtual ligand screening
Creators: name: ÐÐ¾ÑÐµÐ»Ð¾Ð², Ð¡ÐµÑÐ³ÐµÐ¹
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2021
Subjects: nsp
Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½ÑÐ¹ Ð´Ð¾ÐºÐ¸Ð½Ð³
Ð¼Ð¾Ð»ÐµÑÐºÐ»ÑÑÐ½Ð°Ñ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ°
Ð²Ð¸ÑÑÑÐ°Ð»ÑÐ½ÑÐ¹ ÑÐºÑÐ¸Ð½Ð¸Ð½Ð³
ÑÑÑÑÐºÑÑÑÐ°
Ð¼Ð¸Ð½Ð¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ñ ÑÐ½ÐµÑÐ³Ð¸Ð¸
Ð°ÐºÑÐ¸Ð²Ð½ÑÐ¹ ÑÐµÐ½ÑÑ
Ð±Ð¾ÐºÑ
AutoDock Vina
GROMACS
molecular docking
molecular dynamics
virtual screening
structure
energy minimization
active center
box

description: ÐÐ°Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð¿Ð¾ÑÐ²ÑÑÐµÐ½Ð° Ð¿ÑÐ¾Ð²ÐµÐ´ÐµÐ½Ð¸Ñ Ð²Ð¸ÑÑÑÐ°Ð»ÑÐ½Ð¾Ð³Ð¾ ÑÐºÑÐ¸Ð½Ð¸Ð½Ð³Ð° Ð»Ð¸Ð³Ð°Ð½Ð´Ð¾Ð² Ð´Ð»Ñ Ð±ÐµÐ»ÐºÐ¾Ð² Sars-CoV-2, Ð² ÑÐ°ÑÑÐ½Ð¾ÑÑÐ¸, Ð´Ð»Ñ Ð½ÐµÑÑÑÑÐºÑÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð½ÑÑ Ð±ÐµÐ»ÐºÐ¾Ð² nsp5 Ð¸ nsp12. ÐÐ»Ñ ÑÑÐ¾Ð³Ð¾ Ð¿ÑÐ¸Ð¼ÐµÐ½ÑÐ»Ð¸ÑÑ Ð¼ÐµÑÐ¾Ð´Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð³Ð¾ Ð´Ð¾ÐºÐ¸Ð½Ð³Ð° Ð¸ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸. ÐÐ¾Ð»ÐµÐºÑÐ»ÑÑÐ½ÑÐ¹ Ð´Ð¾ÐºÐ¸Ð½Ð³ ÑÐ°ÑÑÑÐ¸ÑÑÐ²Ð°Ð»ÑÑ Ð² Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ðµ AutoDock Vina, Ð² ÑÐ¾ Ð²ÑÐµÐ¼Ñ ÐºÐ°Ðº Ð´Ð»Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸ Ð¸ Ð¼Ð¸Ð½Ð¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ ÑÐ½ÐµÑÐ³Ð¸Ð¸ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð»ÑÑ ÑÐ½Ð¸Ð²ÐµÑÑÐ°Ð»ÑÐ½ÑÐ¹ Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ð½ÑÐ¹ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑ GROMACS. Ð ÐºÐ°ÑÐµÑÑÐ²Ðµ Ð»Ð¸Ð³Ð°Ð½Ð´Ð¾Ð² Ð´Ð»Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð³Ð¾ Ð´Ð¾ÐºÐ¸Ð½Ð³Ð° ÑÐ»ÑÐ¶Ð¸Ð»Ð¸ Ð²ÐµÑÐµÑÑÐ²Ð° Ð¸Ð· Ð±Ð°Ð·Ñ Ð´Ð°Ð½Ð½ÑÑ ZINK15 Ð² ÐºÐ¾Ð»Ð¸ÑÐµÑÑÐ²Ðµ 5901 ÐµÐ´Ð¸Ð½Ð¸ÑÐ°. ÐÐ¾Ð»ÑÑÐµÐ½Ð½ÑÐµ Ð² ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐµ ÑÑÑÑÐºÑÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð½ÑÐµ ÑÐ¿Ð¸ÑÐºÐ¸ Ð»Ð¸Ð³Ð°Ð½Ð´Ð¾Ð² Ð¸Ð· Ð±Ð°Ð·Ñ Ð´Ð°Ð½Ð½ÑÑ Ð¼Ð¾Ð¶Ð½Ð¾ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°ÑÑ Ð´Ð»Ñ Ð¾ÑÐ±Ð¾ÑÐ° Ð¿Ð¾ÑÐµÐ½ÑÐ¸Ð°Ð»ÑÐ½ÑÑ Ð¸Ð½Ð³Ð¸Ð±Ð¸ÑÐ¾ÑÐ¾Ð² Ñ Ð¿Ð¾ÑÐ»ÐµÐ´ÑÑÑÐ¸Ð¼ ÑÐ°ÑÑÑÑÐ¾Ð¼ ÐºÐ¾Ð½ÑÑÐ°Ð½Ñ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð² ÑÐ°ÑÑÐ²Ð¾ÑÐ°Ñ Ñ ÑÐµÐºÐ¾Ð¼Ð±Ð¸Ð½Ð°Ð½ÑÐ½ÑÐ¼Ð¸ Ð±ÐµÐ»ÐºÐ°Ð¼Ð¸. ÐÑÐ¾Ð²ÐµÐ´ÐµÐ½Ð¸Ðµ Ð¿ÑÐ¾ÑÐµÐ´ÑÑÑ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸ Ð¿Ð¾Ð·Ð²Ð¾Ð»Ð¸Ð»Ð¾ Ð¾ÑÐµÐ½Ð¸ÑÑ Ð²Ð·Ð°Ð¸Ð¼Ð¾Ð´ÐµÐ¹ÑÑÐ²Ð¸Ðµ Ð±ÐµÐ»ÐºÐ° nsp7, Ð¿ÑÐ¾ÑÐµÐ´ÑÐµÐ³Ð¾ Ð¿ÑÐµÐ´Ð²Ð°ÑÐ¸ÑÐµÐ»ÑÐ½ÑÑ Ð¼Ð¸Ð½Ð¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ñ ÑÐ½ÐµÑÐ³Ð¸Ð¸, Ñ Ð½ÐµÑÐºÐ¾Ð»ÑÐºÐ¸Ð¼Ð¸ ÑÑÐ°Ð³Ð¼ÐµÐ½ÑÐ°Ð¼Ð¸ Ð¿Ð¾ÑÐ»ÐµÐ´Ð¾Ð²Ð°ÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ ÐºÐ¾ÑÐ°ÑÑÐµÐ³Ð¾, ÑÐ¾Ð±Ð°ÑÑÐµÐ³Ð¾ Ð¸ ÑÐ²Ð¸Ð½Ð¾Ð³Ð¾ ÐºÐ¾ÑÐ¾Ð½Ð°Ð²Ð¸ÑÑÑÐ¾Ð² NILYRSLAETR Ð¸ Ð²ÑÐ´ÐµÐ»Ð¸ÑÑ Ð¿Ð¾ÑÐµÐ½ÑÐ¸Ð°Ð»ÑÐ½ÑÐµ ÑÐ°Ð¹ÑÑ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ñ Ð»Ð¸Ð³Ð°Ð½Ð´Ð¾Ð¼. ÐÐ¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð°Ñ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ° ÑÐ°ÐºÐ¶Ðµ Ð¿Ð¾Ð·Ð²Ð¾Ð»Ð¸Ð»Ð° Ð¿ÑÐ¾Ð½Ð°Ð±Ð»ÑÐ´Ð°ÑÑ Ð¾Ð±ÑÐ°Ð·Ð¾Ð²Ð°Ð½Ð¸Ðµ Ð°Ð¼Ð¸Ð»Ð¾Ð¸Ð´Ð¾Ð¿Ð¾Ð´Ð¾Ð±Ð½ÑÑ ÑÐ¸Ð±ÑÐ¸Ð»Ð» Ñ ÑÑÐ°ÑÑÐ¸ÐµÐ¼ NILYRSLAETR.
description: The given work is devoted to the virtual screening of ligands for the Sars-CoV-2 proteins, in particular, for the unstructured proteins nsp5 and nsp12. The methods of molecular docking and molecular dynamics were used. The procedure of Molecular docking has been performed using the AutoDock Vina software. The universal GROMACS software package was used for molecular dynamics and energy minimization. Substances from the ZINK15 database in the amount of 5901 units were used as ligands for molecular docking. The resulting structured ligand lists from the database can be used to select potential inhibitors with subsequent calculation of the binding constants in solutions with recombinant proteins. The molecular dynamics procedure made it possible to evaluate the interaction of the nsp7 protein, which underwent preliminary energy minimization, with several fragments of the sequence of the feline, canine, and porcine NILYRSLAETR coronaviruses and to highlight potential ligadne binding sites. Molecular dynamics also made it possible to observe the formation of amyloid-like fibrils with the participation of NILYRSLAETR.