Molecular dynamics simulations investigation of neocarzinostatin chromophore-releasing pathways from the holo-NCS protein

Zhao, Xinbing; Wang, Song; Gao, Xuefeng; Huang, Xuri; Sun, Chia‐Chung

doi:10.1016/j.jsb.2009.09.004

Cited by 6 publications

(4 citation statements)

References 40 publications

(48 reference statements)

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“…The root mean square inner product (RMSIP) is calculated to measure the dynamic similarity between subspaces in different systems (van Aalten et al, 1996;Zhao et al, 2010), which is defined by their basis vectors (Amadei et al, 1999):…”

Section: Essential Dynamics Analysismentioning

confidence: 99%

Theoretical investigations on the interactions of glucokinase regulatory protein with fructose phosphates

Ling

Yan

Sun

et al. 2016

Computational Biology and Chemistry

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Section: Essential Dynamics Analysismentioning

confidence: 99%

Theoretical investigations on the interactions of glucokinase regulatory protein with fructose phosphates

Ling

Yan

Sun

et al. 2016

Computational Biology and Chemistry

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“…If the modifications are constrained to the warhead, the natural docking and triggering device will not be affected and can be used. In any case, one has to develop a strategy how the enediyne shall differentiate between normal and cancer cells …”

Section: Target‐specific Enediyne Antitumor Drug Candidatesmentioning

confidence: 99%

“…Therefore, computational chemistry plays an important role since it can be used for a better understanding of the mechanism leading to the bioactivity of natural enediynes as well as the monitoring of changes in this mechanism upon modification of the warhead. In view of the size of the natural enediynes, molecular mechanics (MM) investigations have focused on their conformational flexibility . MM calculations however can say little with regard to the biological activity of a natural enediyne because this involves bond formation/cleavage, which can only be described utilizing quantum chemical means.…”

Section: Target‐specific Enediyne Antitumor Drug Candidatesmentioning

confidence: 99%

Enediynes, enyne‐allenes, their reactions, and beyond

Kraka

2013

WIREs Comput Mol Sci

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Enediynes undergo a Bergman cyclization reaction to form the labile 1,4-didehydrobenzene (p-benzyne) biradical. The energetics of this reaction and the related Schreiner-Pascal reaction as well as that of the Myers-Saito and Schmittel reactions of enyne-allenes are discussed on the basis of a variety of quantum chemical and available experimental results. The computational investigation of enediynes has been beneficial for both experimentalists and theoreticians because it has led to new synthetic challenges and new computational methodologies. The accurate description of biradicals has been one of the results of this mutual fertilization. Other results have been the computer-assisted drug design of new antitumor antibiotics based on the biological activity of natural enediynes, the investigation of hetero-and metallo-enediynes, the use of enediynes in chemical synthesis and materials science, or an understanding of catalyzed enediyne reactions. C 2013 John

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“…With the development of Computer Aided Drug Design (CADD), the cycle of drug research and development has greatly shortened, moreover, contributing to the optimization of the molecular structure of inhibitors [6]. In the past ten years, there were many reports on applying CADD technology to screen PTP1B inhibitors from different databases.…”

Section: Introductionmentioning

confidence: 99%

Discovery and study of novel protein tyrosine phosphatase 1B inhibitors

Zhang¹,

Chen²,

Feng³

2017

AIP Conference Proceedings

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Abstract. Protein tyrosine phosphatase 1B (PTP1B) is considered to be a target for therapy of type diabetes and obesity. So it is of great significance to take advantage of a computer aided drug design protocol involving the structured-based virtual screening with docking simulations for fast searching small molecule PTP1B inhibitors. Based on optimized complex structure of PTP1B bound with specific inhibitor of IX1, structured-based virtual screening against a library of natural products containing 35308 molecules, which was constructed based on Traditional Chinese Medicine database@ Taiwan (TCM database@ Taiwan ), was conducted to determine the occurrence of PTP1B inhibitors using the Lubbock module and CDOCKER module from Discovery Studio 3.1 software package. The results were further filtered by predictive ADME simulation and predictive toxic simulation. As a result, 2 good drug-like molecules, namely parabenzoquinone compound 1 and Clavepictine analogue 2 were identified ultimately with the dock score of original inhibitor (IX1) and the receptor as a threshold. Binding model analyses revealed that these two candidate compounds have good interactions with PTP1B. The PTP1B inhibitory activity of compound 2 hasn't been reported before. The optimized compound 2 has higher scores and deserves further study.

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Molecular dynamics simulations investigation of neocarzinostatin chromophore-releasing pathways from the holo-NCS protein

Cited by 6 publications

References 40 publications

Theoretical investigations on the interactions of glucokinase regulatory protein with fructose phosphates

Theoretical investigations on the interactions of glucokinase regulatory protein with fructose phosphates

Enediynes, enyne‐allenes, their reactions, and beyond

Discovery and study of novel protein tyrosine phosphatase 1B inhibitors

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