Page 88 - IMO-2-2

Innovative Medicines & Omics

ORIGINAL RESEARCH ARTICLE
Femtomolar inhibition by a virtually designed

molecule: Pseudoeriocitrin as a potent inhibitor

Dilara Karaman * , Ahmet Onur Girişgin 2 , and Oya Girişgin 3
1
1 Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical
University, Istanbul, Turkey
2 Department of Parasitology, Faculty of Veterinary Medicine, Bursa Uludağ University, Bursa, Turkey
3 Department of Veterinary, Karacabey Vocational School, Bursa Uludağ University, Bursa, Turkey

Abstract

Pseudoeriocitrin is a virtually designed molecule created in silico by assuming
the formation of oxygen radicals in eriocitrin, resulting in a different geometry. It
achieves femtomolar-level inhibition in in silico docking studies, demonstrating
higher inhibitory efficacy than eriocitrin. This study investigated the mechanisms
underlying the extraordinary inhibitory activity of pseudoeriocitrin through a 3D
analysis of potential interactions using an in silico protein-ligand docking method.
Although it is difficult to reach a definitive conclusion, the absence of hydrogen
donors renders the pseudoeriocitrin structure highly toxic. The high binding affinity
of pseudoeriocitrin, which inhibits various proteins at the femtomolar level, with
the lowest inhibition constant value of 3.45 fM, is presumably due to its planar
structure and the abundance of oxygen radicals, which facilitate the formation of
hydrogen bonds with atoms in the active site of the proteins. This study is the first to
*Corresponding author: demonstrate the structure-activity relationship of pseudoeriocitrin through in silico
Dilara Karaman docking method. The results indicate that the large core structure, abundance of
(dilara.karaman@std.yildiz.edu.tr)
oxygen atoms, planar geometry, and femtomolar-level inhibition are interrelated.
Citation: Karaman D, Girişgin The chemical properties resulting from these unique biological properties should
AO, Girişgin O. Femtomolar
inhibition by a virtually designed be examined from multiple perspectives. In addition, further research is required to
molecule: Pseudoeriocitrin as a explore the synthesis of non-radical pseudoeriocitrin.
potent inhibitor. Innov Med Omics.
2025;2(2):82-98.
doi: 10.36922/imo.6026 Keywords: Eriocitrin; Femtomolar inhibition; Molecular docking; Pseudoeriocitrin
Received: November 16, 2024
Revised: February 21, 2025
Accepted: February 25, 2025
Published online: March 24, 2025 1. Introduction
Copyright: © 2025 Author(s).
This is an Open-Access article In a world experiencing rapid advancement in health service technologies, helminthic
distributed under the terms of the infections remain a serious medical concern. According to recent data, approximately
Creative Commons Attribution two billion people worldwide are infected with at least one species of soil-transmitted
License, permitting distribution,
1
and reproduction in any medium, helminthes. Given the side effects of synthetic anthelmintic drugs, which include the
provided the original work is frequent recurrence of infections in areas with poor sanitation – particularly among
properly cited. pre-school-aged children – the need for alternative treatments to replace synthetic
Publisher’s Note: AccScience drugs has become increasingly important. Consequently, the discovery of new
Publishing remains neutral with anthelmintics with fewer side effects is a crucial task. Oxyurid nematode infections,
regard to jurisdictional claims in
published maps and institutional which are transmitted orally and often recur due to autoinfection, predominantly affect
2
affiliations. children and lead to developmental disorders. It is estimated that 400 million people

Volume 2 Issue 2 (2025) 82 doi: 10.36922/imo.6026