Study on dynamic docking process and collision problems of captured-rod docking method

2019 ◽  
Vol 193 ◽  
pp. 106624
Author(s):  
Lingshuai Meng ◽  
Yang Lin ◽  
Haitao Gu ◽  
Tsung-Chow Su
Keyword(s):  
Docking Method ◽  
Dynamic Docking

An Image-based Docking Method for Mobile Robot

ROBOT ◽  
2010 ◽  
Vol 32 (2) ◽  
pp. 166-170
Author(s):  
Fengdong CHEN ◽  
Bingrong HONG
Keyword(s):  
Mobile Robot ◽  
Docking Method

In silico discovery of novel flavonoids as poly ADP ribose polymerase (PARP) inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Ashish Shah ◽  
Ghanshyam Parmar ◽  
Avinash Kumar Seth
Keyword(s):  
Virtual Screening ◽  
In Silico ◽  
Synthetic Lethality ◽  
Parp Inhibitor ◽  
Parp Inhibitors ◽  
Docking Studies ◽  
Docking Score ◽  
Docking Method ◽  
Anti Cancer ◽  
In Silico Toxicity

Background: The concept of synthetic lethality is emerging field in the treatment of cancer and can be applied for new drug development of cancer as it has been already represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. Objectives: In this study we performed virtual screening of 329 flavonoids obtained from Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target (NPACT) database to identify novel PARP inhibitors. Materials and methods: Virtual screening carried out using different In Silico methods which includes molecular docking studies, prediction of druglikeness and In Silico toxicity studies. Results: Fifteen out of 329 flavonoids achieved better docking score as compared to rucaparib which is an FDA approved PARP inhibitor. These 15 hits were again rescored using accurate docking mode and drug-likeliness properties were evaluated. Accuracy of docking method was checked using re-docking. Finally NPACT00183 and NPACT00280 were identified as potential PARP inhibitors with docking score of -139.237 and -129.36 respectively. These two flavonoids were also showed no AMES toxicity and no carcinogenicity which was predicted using admetSAR. Conclusion: Our finding suggests that NPACT00183 and NPACT00280 have promising potential to be further explored as PARP inhibitors.

scholarly journals Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gert-Jan Bekker ◽  
Ikuo Fukuda ◽  
Junichi Higo ◽  
Yoshifumi Fukunishi ◽  
Narutoshi Kamiya
Keyword(s):  
Ligand Binding ◽  
Cancer Progression ◽  
Hydrophobic Interactions ◽  
Binding Mechanism ◽  
Docking Simulations ◽  
Large Conformational Change ◽  
Binding Pockets ◽  
Dynamic Docking ◽  
Site Binding ◽  
Apo State

AbstractWe have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur.

scholarly journals Synthesis of oxadiazole-2-oxide derivatives as potential drug candidates for schistosomiasis targeting SjTGR

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Gongming Li ◽  
Qingqing Guo ◽  
Chao Feng ◽  
Huan Chen ◽  
Wenjiao Zhao ◽  
...  
Keyword(s):  
Schistosoma Japonicum ◽  
Inhibitory Activity ◽  
Pyridine Ring ◽  
New Drugs ◽  
Wild Type ◽  
Drug Candidates ◽  
Structure Activity ◽  
Docking Method ◽  
Antigen Protein ◽  
Thioredoxin Glutathione Reductase

Abstract Background Schistosomiasis is a chronic parasitic disease that affects millions of people’s health worldwide. Because of the increasing drug resistance to praziquantel (PZQ), which is the primary drug for schistosomiasis, developing new drugs to treat schistosomiasis is crucial. Oxadiazole-2-oxides have been identified as potential anti-schistosomiasis reagents targeting thioredoxin glutathione reductase (TGR). Methods In this work, one of the oxadiazole-2-oxides derivatives furoxan was used as the lead compound to exploit a series of novel furoxan derivatives for studying inhibitory activity against both recombinant Schistosoma japonicum TGR containing selenium (rSjTGR-Sec) and soluble worm antigen protein (SWAP) containing wild-type Schistosoma japonicum TGR (wtSjTGR), in order to develop a new leading compound for schistosomiasis. Thirty-nine novel derivatives were prepared to test their activity toward both enzymes. The docking method was used to detect the binding site between the active molecule and SjTGR. The structure–activity relationship (SAR) of these novel furoxan derivatives was preliminarily analyzed. Results It was found that several new derivatives, including compounds 6a–6d, 9ab, 9bd and 9be, demonstrated greater activity toward rSjTGR-Sec or SWAP containing wtSjTGR than did furoxan. Interestingly, all intermediates bearing hydroxy (6a–6d) showed excellent inhibitory activity against both enzymes. In particular, compound 6d with trifluoromethyl on a pyridine ring was found to have much higher inhibition toward both rSjTGR-Sec (half-maximal inhibitory concentration, IC50,7.5nM) and SWAP containing wtSjTGR (IC50 55.8nM) than furoxan. Additionally, the docking method identified the possible matching sites between 6d and Schistosoma japonicum TGR (SjTGR), which theoretically lends support to the inhibitory activity of 6d. Conclusion The data obtained herein showed that 6d with trifluoromethyl on a pyridine ring could be a valuable leading compound for further study.

Study on the Substrate Specificity of Xylose Isomerase N91D Mutant from Thermus thermophilus HB8 by Molecular Simulation

2011 ◽  
Vol 236-238 ◽  
pp. 968-973
Author(s):  
Wei Xu ◽  
Rong Shao ◽  
Yan Li ◽  
Ming Yan ◽  
Ping Kai Ouyang
Keyword(s):  
Substrate Specificity ◽  
Catalytic Mechanism ◽  
Molecular Design ◽  
Thermus Thermophilus ◽  
Xylose Isomerase ◽  
Homology Model ◽  
Complex Model ◽  
Structural Mechanism ◽  
Docking Method ◽  
Conserved Residue

Compared withThermus thermophilusHB8 xylose isomerase(TthXI), the increase of the substrate specificity on D-xylose of its N91D mutant (TthXI-N91D) was observed in the previous study. In order to clarify the structural mechanism of TthXI-N91D, the complex model of TthXI with D-xylose was constructed by molecular docking method. The TthXI-N91D homology model was built by WATH IF5.0 based on the above complex. The results indicate that the distance between the conserved residue H53 NE2 and D-xylose O5 has decreased in 0.083 nm in the TthXI-N91D active site. The short distance is propitious to transfer the hydrogen atom during the open ring process of substrate. At the same time, the distance between the conserved residue T89 OG1, involving in combining glucose, and D-xylose C5 has reduced 0.133 nm. The shrunken space has an unfavorable effect on accommodating the larger glucose than xylose, and lead to the enhanced specificity for D-xylose.The above phenomenon maybe the main reason for explaining that TthXI-N91D is easy to combine D-xylose showing enhanced specificity. The results paly an important role in understanding the catalytic mechanism of xylose isomerase and provides the base for its molecular design.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Bhringraj Derived Phytochemicals against Pneumonia

2020 ◽  
pp. 93-96
Author(s):  
Debajani Tripathy ◽  
Chandana Adhikari ◽  
Mukundjee Pandey ◽  
Dipankar Bhattacharayay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Glutamic Acid ◽  
Interaction Energy ◽  
Plant Extract ◽  
Klebsiella Pneumonia ◽  
Discovery Studio ◽  
Docking Method ◽  
Dehydrogenase Enzyme ◽  
Molecular Docking Method

Phytochemicals from Bhringaraj plant extract are traditionally used to cure Pneumonia. It is caused by Klebsiella pneumonia. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that glutamic acid can effectively deactivate the dehydrogenase enzyme, thereby interrupting the life cycle of the organism.

scholarly journals Trigonella foenum-graecum Derived Phytochemicals against Tuberculosis

2020 ◽  
pp. 121-124
Author(s):  
Bidyashree Tripathy ◽  
Elina Sahoo ◽  
Sidhartha Ray ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Interaction Energy ◽  
Dihydrofolate Reductase ◽  
Plant Extract ◽  
Discovery Studio ◽  
Trigonella Foenum Graecum ◽  
Docking Method ◽  
Molecular Docking Method

Phytochemicals from Trigonella foenum-graecum plant extract are traditionally used to cure Tuberculosis. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that this plant extract can effectively deactivate the dihydrofolate reductase enzyme thereby interrupting the life cycle of the organism.

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