Abstract:
:Non-homologous end joining (NHEJ) is a major DNA double strand breaks (DSBs) repair pathway that maintains genome integrity. However, this pathway may reduce radiotherapy efficacy by repairing DSBs on cancer cells. This research reported a computer-aided drug design (CADD) method to identify novel inhibitors from traditional Chinese medicine (TCM) that disrupt NHEJ. We aim to inhibit Ku86, the initiator of NHEJ. By integrating binding energy evaluation and molecular dynamics simulation methods, we reported glycyrrhizic acid, macedonoside C, lithospermic acid, and salvianolic acid B as potential Ku86 inhibitors. All four TCM compounds show low binding energy and stable binding poses to Ku86. The carboxyl groups on a ligand are the major binding region by forming salt bridges at Ku86 binding sites. Additional features were defined by a carbonyl group or a dihydroxyphenyl group that form additional hydrogen bond or pi-cation respectively with the ligand binding site on Ku86. These features strengthen the binding affinity between Ku86 and the potential TCM ligand. We reported all four TCM compounds are potential Ku86 inhibitors and may be used to enhance radiotherapy for cancer treatment.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Sun MF,Chang TT,Chang KW,Huang HJ,Chen HY,Tsai FJ,Lin JG,Chen CYdoi
10.1080/07391102.2011.10508616subject
Has Abstractpub_date
2011-06-01 00:00:00pages
895-906issue
6eissn
0739-1102issn
1538-0254pii
c4310/Blocking-the-DNA-Repair-System-by-Traditionajournal_volume
28pub_type
杂志文章abstract::It is generally believed that base-pair stacking interaction in DNA double helix is one of the strongest interactions that governs sequence directed structural variability. However, X-ray crystal structures of some base-paired doublet sequences have been seen to adopt different structures when flanked by different bas...
journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.2000.10506645
更新日期:2000-08-01 00:00:00
abstract::Amyotrophic lateral sclerosis (ALS), a progressive motor-neurone disease, affects individuals usually aged between 50 and 70 years. C21orf2, recently identified as the new ALS susceptibility gene, harbours rare missense mutations that cause this fatal disease. We used bioinformatics and molecular modelling approaches ...
journal_title:Journal of biomolecular structure & dynamics
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journal_title:Journal of biomolecular structure & dynamics
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abstract::Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...
journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/073911012010525025
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journal_title:Journal of biomolecular structure & dynamics
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2002.10506789
更新日期:2002-04-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.2002.10506844
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.827132
更新日期:2014-01-01 00:00:00
abstract::In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α-, and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic, and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic cont...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
doi:10.1080/07391102.2017.1411833
更新日期:2018-12-01 00:00:00
abstract::Inosine 5' monophosphate dehydrogenase (IMPDH II) is a key enzyme involved in the de novo biosynthesis pathway of purine nucleotides and is also considered to be an excellent target for cancer inhibitor design. The conserve R 322 residue (in human) is thought to play some role in the recognition of inhibitor and cofac...
journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.2009.10507304
更新日期:2009-10-01 00:00:00
abstract::Among the plant constituents of Clerodendrum colebrookianum Walp., acteoside, martinoside, and osmanthuside β6 interact with ROCK, a drug target for cancer. In this study, aglycone fragments of these plant constituents (caffeic acid, ferulic acid, and p-coumaric acid) along with the homopiperazine ring of fasudil (sta...
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abstract::Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked whic...
journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.2015.1064831
更新日期:2016-05-01 00:00:00
abstract::Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrost...
journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.2013.800994
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abstract::The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentati...
journal_title:Journal of biomolecular structure & dynamics
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更新日期:2005-06-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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更新日期:2019-04-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
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abstract::The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information St...
journal_title:Journal of biomolecular structure & dynamics
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更新日期:2008-04-01 00:00:00
abstract::A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecyl...
journal_title:Journal of biomolecular structure & dynamics
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更新日期:2014-01-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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更新日期:1985-10-01 00:00:00
abstract::Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,收录出版
doi:10.1080/07391102.2011.10507386
更新日期:2011-10-01 00:00:00
abstract::Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes a three-state prediction first (ordered residue...
journal_title:Journal of biomolecular structure & dynamics
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