Computational Investigation of 5-Ethynyl-2’-deoxyuridine (EdU) as a Biologically Active Nucleoside Analogue: Insights from Molecular Docking, ADMET Profiling, and DFT Analyses

Meryem Alp

Makale detayları

Computational Investigation of 5-Ethynyl-2’-deoxyuridine (EdU) as a Biologically Active Nucleoside Analogue: Insights from Molecular Docking, ADMET Profiling, and DFT Analyses

Yazarlar:

Meryem Alp

Yayıncı:

Zonguldak Bulent Ecevit University

Ana Başlıklar:

Endokrinoloji | Sağlık Fiziği

Dergi:

Yükseköğretim ve Bilim Dergisi Vol.15 Issue 2, pp.310-321

Belge Tipi:

Makale

Yayın Tarihi:

8/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001357713

pISSN:

2146-5959

Anahtar kelimeler:

Özet:

 This study presents a comprehensive computational investigation of the molecule 5-ethynyl-2-deoxyuridine EdU, a thymidine analogue of considerable biological importance. The investigation includes quantum chemical analyses, molecular docking, and pharmacokinetic evaluation to assess the structural, electronic, and biological properties of EdU. Initially, the molecular geometry of EdU was optimized using Density Functional Theory DFT, providing a basis for deeper electronic structure evaluations. Topological analyses, including Electron Localization Function ELF and Localized Orbital Locator LOL, were performed to explore the distribution of electron density and bonding properties within the molecule. These visual and quantitative descriptors contributed to a clearer understanding of the reactivity and stability of the molecule. The pharmacokinetic behavior of EdU and its similarity to the drug was evaluated through in silico ADME absorption, distribution, metabolism, and excretion modeling. Using internet-based platforms such as SwissADME and admetSAR, various parameters were evaluated to determine the potential of the molecule as an orally active compound and its compliance with established drug similarity rules. Toxicological properties were further investigated using predictive tools to estimate acute and environmental toxicity risks. Molecular docking simulations were performed to investigate the interaction between EdU and the selected proteins alpha-amylase and alpha-glucosidase, selected for their endocrinological importance, providing insights into possible binding mechanisms and structural compatibility. Overall, this study uses a multidisciplinary computational approach to provide a detailed theoretical profile of EdU, contributing to the understanding of its chemical behavior and potential applications in biomedical research.

 This study presents a comprehensive computational investigation of the molecule 5-ethynyl-2-deoxyuridine EdU, a thymidine analogue of considerable biological importance. The investigation includes quantum chemical analyses, molecular docking, and pharmacokinetic evaluation to assess the structural, electronic, and biological properties of EdU. Initially, the molecular geometry of EdU was optimized using Density Functional Theory DFT, providing a basis for deeper electronic structure evaluations. Topological analyses, including Electron Localization Function ELF and Localized Orbital Locator LOL, were performed to explore the distribution of electron density and bonding properties within the molecule. These visual and quantitative descriptors contributed to a clearer understanding of the reactivity and stability of the molecule. The pharmacokinetic behavior of EdU and its similarity to the drug was evaluated through in silico ADME absorption, distribution, metabolism, and excretion modeling. Using internet-based platforms such as SwissADME and admetSAR, various parameters were evaluated to determine the potential of the molecule as an orally active compound and its compliance with established drug similarity rules. Toxicological properties were further investigated using predictive tools to estimate acute and environmental toxicity risks. Molecular docking simulations were performed to investigate the interaction between EdU and the selected proteins alpha-amylase and alpha-glucosidase, selected for their endocrinological importance, providing insights into possible binding mechanisms and structural compatibility. Overall, this study uses a multidisciplinary computational approach to provide a detailed theoretical profile of EdU, contributing to the understanding of its chemical behavior and potential applications in biomedical research.

 This study presents a comprehensive computational investigation of the molecule 5-ethynyl-2-deoxyuridine EdU, a thymidine analogue of considerable biological importance. The investigation includes quantum chemical analyses, molecular docking, and pharmacokinetic evaluation to assess the structural, electronic, and biological properties of EdU. Initially, the molecular geometry of EdU was optimized using Density Functional Theory DFT, providing a basis for deeper electronic structure evaluations. Topological analyses, including Electron Localization Function ELF and Localized Orbital Locator LOL, were performed to explore the distribution of electron density and bonding properties within the molecule. These visual and quantitative descriptors contributed to a clearer understanding of the reactivity and stability of the molecule. The pharmacokinetic behavior of EdU and its similarity to the drug was evaluated through in silico ADME absorption, distribution, metabolism, and excretion modeling. Using internet-based platforms such as SwissADME and admetSAR, various parameters were evaluated to determine the potential of the molecule as an orally active compound and its compliance with established drug similarity rules. Toxicological properties were further investigated using predictive tools to estimate acute and environmental toxicity risks. Molecular docking simulations were performed to investigate the interaction between EdU and the selected proteins alpha-amylase and alpha-glucosidase, selected for their endocrinological importance, providing insights into possible binding mechanisms and structural compatibility. Overall, this study uses a multidisciplinary computational approach to provide a detailed theoretical profile of EdU, contributing to the understanding of its chemical behavior and potential applications in biomedical research.

 Bu çalışma, kayda değer biyolojik öneme sahip bir timidin analoğu olan 5-etinil-2-deoksiüridin EdU molekülünün kapsamlı bir hesaplamalı incelemesini sunmaktadır. Araştırma, EdUnun yapısal, elektronik ve biyolojik özelliklerini değerlendirmek için kuantum kimyasal analizleri, moleküler yerleştirme ve farmakokinetik değerlendirme içermektedir. Başlangıçta, EdUnun moleküer geometrisi Yoğunluk Fonksiyonel Teorisi DFT kullanılarak optimize edilmiş ve daha derin elektronik yapı değerlendirmeleri için bir temel sağlanmıştır. Elektron Lokalizasyon Fonksiyonu ELF ve Lokalize Orbital Konumlandırıcı LOL dahil olmak üzere topolojik analizler, molekül içindeki elektron yoğunluğu ve bağlanma özelliklerinin dağılımını keşfetmek için yapılmıştır. Bu görsel ve nicel tanımlayıcılar, molekülün reaktivitesinin ve stabilitesinin daha net anlaşılmasına katkıda bulunmuştur. EdUnun farmakokinetik davranışı ve ilaca benzerliği, in silico ADME emilim, dağılım, metabolizma ve atılım modellemesi yoluyla değerlendirilmiştir. SwissADME ve admetSAR gibi internet tabanlı platformlar kullanılarak, molekülün oral olarak aktif bir bileşik olarak potansiyelini ve yerleşik ilaç benzerliği kurallarına uygunluğunu belirlemek için çeşitli parametreler değerlendirilmiştir. Toksikolojik özellikler, akut ve çevresel toksisite risklerini tahmin etmek için öngörücü araçlar kullanılarak daha fazla araştırılmıştır. EdU ile endokrinolojik öneme sahip olduğu için seçilen alfa-amilaz ve alfa-glukosidaz seçil proteinleri arasındaki etkileşimi araştırmak için moleküler yerleştirme simülasyonları gerçekleştirilerek olası bağlanma mekanizmaları ve yapısal uyumluluk hakkında içgörüler sağlanmıştır. Genel olarak, bu çalışma EdUnun ayrıntılı bir teorik profilini sunmak için multidisipliner bir hesaplama yaklaşımı kullanmakta, kimyasal davranışının ve biyomedikal araştırmalardaki potansiyel uygulamalarının anlaşılmasına katkıda bulunmaktadır.

Makale detayları

Computational Investigation of 5-Ethynyl-2’-deoxyuridine (EdU) as a Biologically Active Nucleoside Analogue: Insights from Molecular Docking, ADMET Profiling, and DFT Analyses

Yazarlar:

Meryem Alp

Yayıncı:

Zonguldak Bulent Ecevit University

Ana Başlıklar:

Endokrinoloji | Sağlık Fiziği

Dergi:

Yükseköğretim ve Bilim Dergisi Vol.15 Issue 2, pp.310-321

Belge Tipi:

Makale

Yayın Tarihi:

8/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001357713

pISSN:

2146-5959

5-Ethynyl-2’-deoxyuridine

DFT

Quantum chemical calculation

Topological analyses

Molecular docking5-Etinil-2

DFT

Kuantum kimyasal inceleme

Topolojik analiz

Moleküler yerleştirme çalışması

Sayı

Makale detayları

Yazarlar: Meryem Alp

Yayıncı: Zonguldak Bulent Ecevit University

Ana Başlıklar: Endokrinoloji | Sağlık Fiziği

Dergi: Yükseköğretim ve Bilim Dergisi Vol.15 Issue 2, pp.310-321

Belge Tipi: Makale

Yayın Tarihi: 8/2025

Belge Dili: İngilizce

Document ID (Org No.): 2001357713

pISSN: 2146-5959

Sayı

Yazarlar:

Meryem Alp

Yayıncı:

Zonguldak Bulent Ecevit University

Ana Başlıklar:

Endokrinoloji | Sağlık Fiziği

Dergi:

Yükseköğretim ve Bilim Dergisi Vol.15 Issue 2, pp.310-321

Belge Tipi:

Makale

Yayın Tarihi:

8/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001357713

pISSN:

2146-5959