Application of reverse docking for target prediction of marine compounds with anti-tumor activity

Chen, Fangling; Wang, Zhuoya; Wang, Chaoyi; Xu, Qingliang; Liang, Jiazhen; Xu, Ximing; Yang, Jinbo; Wang, Chang‐Yun; Jiang, Tao; Yu, Rilei

doi:10.1016/j.jmgm.2017.09.015

Cited by 32 publications

(29 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For example, Grinter et al 29 explored the potential target oxidized squalene cyclase (OSC) of PRIMA-1 by using the reverse docking software package Mdock. Also, Chen et al 30 applied reverse docking technique to discover targeted proteins of marine compounds with anti-tumour activity. Furthermore, Chen et al 30 also indicated that reverse docking can be complementary with in vitro assays as an operative method of target fishing.…”

Section: Molecular Docking Databasesmentioning

confidence: 99%

“…Also, Chen et al 30 applied reverse docking technique to discover targeted proteins of marine compounds with anti-tumour activity. Furthermore, Chen et al 30 also indicated that reverse docking can be complementary with in vitro assays as an operative method of target fishing. Finally, we reflected that exploring relevant mechanism of action or side effect profile by structural biology analysis 31 such as the pocket analysis 32 ; could significantly benefit the novel drug design.…”

Section: Molecular Docking Databasesmentioning

confidence: 99%

See 1 more Smart Citation

Molecular Docking Software’s Applications and Basic Challenges Faced: A Review

Sawhney¹,

Singh²

2020

Int Res J Pharm

View full text Add to dashboard Cite

Molecular docking shows a very important role in the rational design of drugs. Method of molecular docking calculates the preferred orientation of one molecule with the second molecule when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules. Docking is normally used to predict the binding orientation of small molecule drug candidates to their protein targets in order to predict the affinity and activity of the small molecule. Given the biological and pharmaceutical importance of molecular docking, considerable efforts have been directed towards improving the methods used to calculate docking. The docking process simulates the ligand-protein pairwise interaction and the energies are calculated. There are three types of Docking: Protein-Protein Docking, Protein-Ligand Docking and Protein-Protein and Protein-Ligand docking. Molecular docking software includes Auto dock, Flex-X, Glide, Gold, ZDOCK, RDOCK, LeDOCK, Dock, Auto dock Vina, Mdock etc. The present review accumulates the characteristics and applications of the different software used and the basic challenges faced in molecular docking studies.

show abstract

Section: Molecular Docking Databasesmentioning

confidence: 99%

Section: Molecular Docking Databasesmentioning

confidence: 99%

Molecular Docking Software’s Applications and Basic Challenges Faced: A Review

Sawhney¹,

Singh²

2020

Int Res J Pharm

View full text Add to dashboard Cite

show abstract

“…Molecular docking has been the major SB methodology to predict affinities to macromolecular targets, to interpret binding modes, and to assist in the design of drug leads. Several recent publications illustrate the application of the method to MNPs [ 127 , 128 , 129 , 138 , 152 , 153 , 154 , 155 , 156 , 157 , 158 , 159 , 160 , 161 , 162 , 163 , 164 , 165 , 166 , 167 , 168 , 169 , 170 , 171 ], and some representative examples are here described.…”

Section: Computer-aided Drug Design (Cadd)mentioning

confidence: 99%

Computational Methodologies in the Exploration of Marine Natural Product Leads

Pereira

Aires-de-Sousa

2018

Marine Drugs

View full text Add to dashboard Cite

Computational methodologies are assisting the exploration of marine natural products (MNPs) to make the discovery of new leads more efficient, to repurpose known MNPs, to target new metabolites on the basis of genome analysis, to reveal mechanisms of action, and to optimize leads. In silico efforts in drug discovery of NPs have mainly focused on two tasks: dereplication and prediction of bioactivities. The exploration of new chemical spaces and the application of predicted spectral data must be included in new approaches to select species, extracts, and growth conditions with maximum probabilities of medicinal chemistry novelty. In this review, the most relevant current computational dereplication methodologies are highlighted. Structure-based (SB) and ligand-based (LB) chemoinformatics approaches have become essential tools for the virtual screening of NPs either in small datasets of isolated compounds or in large-scale databases. The most common LB techniques include Quantitative Structure–Activity Relationships (QSAR), estimation of drug likeness, prediction of adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, similarity searching, and pharmacophore identification. Analogously, molecular dynamics, docking and binding cavity analysis have been used in SB approaches. Their significance and achievements are the main focus of this review.

show abstract

“…Reverse molecular docking refers to the docking of a small molecule drug in a group of potential binding cavities of clinically relevant large molecule targets. Through detailed analysis of its binding characteristics, the potential small molecule targets are identified and ranked according to the binding tightness [28,29]. In this study, network pharmacology and molecular docking were utilized to elucidate the mechanisms of fucosterol treatment of NSCLC, providing new ideas for the treatment of NSCLC and promoting the development of new drugs.…”

Section: Introductionmentioning

confidence: 99%

Exploration in the mechanism of fucosterol for the treatment of non-small cell lung cancer Based on network pharmacology and molecular docking

Lin

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: It has been demonstrated that fucosterol induces a therapeutic effect on cancer. However, the molecular mechanisms underlying the effects of fucosterol in the treatment of non-small cell lung cancer are still unclear.Methods: In this study, pharmMapper and GeneCards databases were utilized to gather the prediction of fucosterol targets and NSCLC-related targets. The mechanisms of fucosterol against NSCLC were identified in DAVID6.8 by enrichment analysis of GO and KEGG, and protein-protein interaction data was obtained from Sting Database. Molecular docking was used to predict the docking of GRB2. Moreover, the relationship of GRB2 expression and immune infiltrates was analyzed by TIMER database.Results: The results suggest that fucosterol acts against by candidate targets, such as MAPK1, EGFR, GRB2, IGF2, MAPK8 and SRC, which regulate biological processes including negative regulation of apoptotic process, peptidyl-tyrosine phosphorylation, positive regulation of cell proliferation. The Raf / MEK / ERK signaling pathway initiated by GRB2 maybe the most significant pathway for fucosterol to treat NSCLC.Conclusions: These results show that GRB2 is the key target for fucosterol in the treatment of NSCLC, which laying a theoretical foundation for further research and providing scientific support for the development of new drugs.

show abstract

Application of reverse docking for target prediction of marine compounds with anti-tumor activity

Cited by 32 publications

References 24 publications

Molecular Docking Software’s Applications and Basic Challenges Faced: A Review

Molecular Docking Software’s Applications and Basic Challenges Faced: A Review

Computational Methodologies in the Exploration of Marine Natural Product Leads

Exploration in the mechanism of fucosterol for the treatment of non-small cell lung cancer Based on network pharmacology and molecular docking

Contact Info

Product

Resources

About