Piridin Türevi Bileşiğin Bütüncül Deneysel ve Hesaplamalı İncelemesi: X-ışını, DFT ve Docking Çalışmaları

Abstract

Bu çalışmada, piridinon türevi bir bileşiğin yapısal karakterizasyonu ve hesaplamalı analizi bütüncül deneysel ve teorik yöntemlerle gerçekleştirilmiştir. Tek kristal X-ışını kırınımı (SC-XRD) sonuçları, molekülün güçlü N–H···O hidrojen bağları ve zayıf π–π etkileşimleriyle stabilize olmuş, belirgin şekilde düzlemsel olmayan bir konformasyon sergilediğini göstermiştir. Yoğunluk Fonksiyonel Teorisi (DFT) hesaplamaları, yüksek moleküler kararlılığı gösteren geniş bir HOMO–LUMO enerji aralığı (7.12 eV) ortaya koymuştur. Moleküler docking simülasyonları, DNA replikasyonunda görev alan Topoizomeraz II (PDB ID: 3QX3) enzimi üzerinde gerçekleştirilmiş; bileşiğin –5.23 kcal/mol bağlanma enerjisiyle orta düzeyde bir afinite gösterdiği belirlenmiştir. Van der Waals, hidrojen bağı ve π–π etkileşimlerinin hâkim olduğu bu bağlanma, ligandın enzim aktif bölgesinde kararlı bir şekilde konumlandığını göstermektedir. Elde edilen sonuçlar, sentezlenen bileşiğin yapısal kararlılığını, elektronik özelliklerini ve biyolojik etkileşim potansiyelini ortaya koyarak gelecekteki yapı–etki ilişkisi ve antikanser çalışmalarına ışık tutmaktadır.

Keywords

• Piridin türevi
• X-ışını kristalografisi
• DFT hesaplamaları
• Moleküler docking
• Topoizomeraz II inhibisyonu

Supporting Institution

Dokuz Eylül Üniversitesi

Project Number

2010.KB.FEN.13

Ethical Statement

Bu çalışma insan katılımcıları veya hayvan deneylerini içermediğinden, etik onay gerekli değildir.

Thanks

Yazarlar, Dokuz Eylül Üniversitesi'ne Agilent Xcalibur Eosdifraktometre (2010.KB.FEN.13 numaralı Üniversite Araştırma hibesi kapsamında satın alınmıştır) ve Gauss Yazılım Programı'nı kullanma imkanı sağladığı için teşekkür eder.

Integrated Experimental and Computational Investigation of a Pyridine Derivative Compound: X-ray, DFT, and Docking Studies

Abstract

In this study, a pyridinone-based compound was structurally characterized and computationally analyzed using integrated experimental and theoretical methods. The single-crystal X-ray diffraction (SC-XRD) results confirmed that the molecule adopts a non-planar conformation stabilized by strong N–H···O hydrogen bonds and weak π–π interactions. Density Functional Theory (DFT) calculations reveal a wide HOMO–LUMO energy gap (7.12 eV), indicative of high molecular stability and polar nature. Molecular docking simulations were carried out against Topoisomerase II (PDB ID: 3QX3) to investigate the binding affinity and interaction profile. The compound exhibited a moderate binding energy of –5.23 kcal/mol, dominated by van der Waals, hydrogen bonding, and π–π stacking interactions, suggesting a stable binding orientation within the enzyme’s active site. The combined results highlight the structural stability, electronic properties, and biointeraction potential of the synthesized ligand, supporting its relevance for future structure–activity relationship and anticancer studies.

Keywords

• Pyridine derivative
• X-ray crystallography
• DFT calculations
• Molecular docking
• Topoisomerase II inhibition

Supporting Institution

Dokuz Eylul University

Project Number

2010.KB.FEN.13

Ethical Statement

This study did not involve human participants or animal experiments; therefore, ethical approval was not required.

Thanks

The authors thank the Dokuz Eylul University for the use of the Agilent Xcalibur Eosdiffractometer (purchased under University Research grant no. 2010.KB.FEN.13) and the Gaussian Software Programme.

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