Ligand binding constants of the cucurbit[7]uril predicted with molecular docking: a theoretical study

A binding stability order predicting, molecular docking based fast technique was developed for host--guest complexes. Molecular descriptors were applied to ligand molecules to make the binding energy based docking scoring functions more efficient and reach the $\pm $0.50 log K unit theoretical precision for predictions. The goal of this work was to model complexes of cucurbit[7]uril (CB7) as a host molecule with different local anesthetics and choline and phosphonium choline molecules. The guest molecules were docked into the cavity of CB7. The binding free energy maps were correlated by Contact, Grid-Based, Hawkins GB/SA, and AMBER docking scores obtained from UCSF DOCK software. The guest molecules were clustered by the scores. Linear correlations on the ln K - docking score plots were characterized on the learning set and log K was reproduced on the test set within an accuracy of $\pm $0.92 log K units.
Turkish Journal of Chemistry-Cover
  • ISSN: 1300-0527
  • Yayın Aralığı: Yılda 6 Sayı
  • Yayıncı: TÜBİTAK
Sayıdaki Diğer Makaleler

Synthesis and evaluation of novel 1,3,4-thiadiazole–fluoroquinolone hybrids as antibacterial, antituberculosis, and anticancer agents

Zühtü Tanıl KOCAGÖZ, Fikrettin ŞAHİN, Aslı DEMİRCİ, Kaan Gökçe KARAYEL, Sinem ÖKTEM OKULLU, Nihan ÜNÜBOL, İlkay KÜÇÜKGÜZEL, Esra TATAR, Pakize Neslihan TAŞLI

Synthesis and characterization of novel unsymmetrical phthalocyanine/TiO2 composites and their evaluation as photocatalysts for degradation of 4-chlorophenol under visible light

Görkem GEZEK, Yunus Alp SÜTCÜLER, Altuğ Mert SEVİM, Yaghub MAHİANİ

Electrochemical behavior and voltammetric determination of some nitro-substituted benzamide compounds

Tuğba GÜNGÖR, Ferah CÖMERT ÖNDER, Yusuf DİLGİN, Mehmet AY, Ozlem SAĞLAM

Recent advances in organ-on-a-chip technologies and future challenges: a review

Salim EROL, Ali AKPEK, Hüseyin AVCI, Fatma DOĞAN GÜZEL

The first synthesis and antioxidant and anticholinergic activities of 1-(4,5-dihydroxyb enzyl)pyrrolidin-2-one derivative bromophenols including natural products

Abdullah MENZEK, İlhami GÜLÇİN, Mohsen REZAI, Çetin BAYRAK, Parham TASLIMI

A simple automated microplate metho d for determining reducing sugars in fo o d extracts and synthetic serum using cupric-neo cuproine as reductant

Reşat APAK, Kevser SÖZGEN BAŞKAN, Esma TÜTEM, Mustafa BENER, Furkan Burak ŞEN, Esin AKYÜZ

Enhanced electrocatalytic activity of copper phthalocyanine/multiwalled carbon nanotube composite electrode via Pt nanoparticle modification for oxygen reduction

Zekerya DURSUN, Çağrı Ceylan KOÇAK

Photocatalytic degradation of the herbicide quinclorac in water using Mn (III) salen and solar light

Qingru ZENG, Yan ZHANG, Yisi YANG

Şule Atahan EVRENK

Computational investigation of intramolecular reorganization energy in diketopyrrolopyrrole (DPP) derivatives

Şule ATAHAN EVRENK