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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Dipeptidyl peptidase 4 (DPP-4) is a serine protease widely distributed in the body. It's involved in the inactivation of GLP-1 and GIP hormones, which are crucial for insulin regulation. DPP-4 inhibitors, such as sitagliptin (Januvia), saxagliptin (Onglyza), linagliptin (Tradjenta), alogliptin (Nesina), and vildagliptin (Galvus), help increase the proportion of active GLP-1, enhancing insulin secretion. These inhibitors work by competitively binding to DPP-4. This binding causes a...
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Enzyme Inhibition01:30

Enzyme Inhibition

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Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.
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Related Experiment Video

Updated: Oct 25, 2025

A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9
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A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9

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Finding inhibitors for PCSK9 using computational methods.

Rida Zainab1, Afshan Kaleem1, Michał B Ponczek2

  • 1Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan.

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|August 5, 2021
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Summary

This study identified potential drug candidates targeting PCSK9, a key factor in atherosclerosis. (S)-canadine showed the most stable interaction, suggesting its potential for developing new PCSK9 inhibitors against atherosclerosis.

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Area of Science:

  • Biochemistry
  • Pharmacology
  • Computational Chemistry

Background:

  • Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a critical target for atherosclerosis drug development.
  • PCSK9's interaction with the low-density lipoprotein receptor promotes atherosclerosis.
  • Understanding protein-ligand interactions is crucial for elucidating pharmacological mechanisms.

Purpose of the Study:

  • To discover novel inhibitory drug candidates targeting PCSK9.
  • To identify compounds with potential pharmacological action against atherosclerosis.
  • To explore the molecular interactions between potential inhibitors and PCSK9.

Main Methods:

  • Pharmacophore modeling using PharmaGist with ACE inhibitors.
  • Screening the ZINC database using ZINCPHARMER.
  • Molecular docking and dynamics simulations to assess protein-ligand interactions and stability.
  • Analysis of pharmacokinetic properties and oral bioavailability.

Main Results:

  • Identified top 10 drug candidates against PCSK9 with binding energies from -9.8 to -8.2 kcal·mol-1.
  • Discovered plant-derived compounds like (S)-canadine and hesperetin, and labetalol as potential inhibitors.
  • Molecular dynamics confirmed stable protein-ligand complexes, with (S)-canadine-PCSK9 exhibiting the lowest RMSD.
  • (S)-canadine demonstrated the most stable complex formation.

Conclusions:

  • The study identified (S)-canadine as a highly promising candidate for PCSK9 inhibition.
  • (S)-canadine may serve as a potential therapeutic agent for atherosclerosis.
  • Further in vitro research is warranted for developing new PCSK9 inhibitory drugs.