Computational Study on Novel Natural Inhibitors Targeting Janus Kinase 3

2021 ◽  
Author(s):  
Sheng Zhong ◽  
Weihang Li ◽  
Bo Wu ◽  
Yujia Zou ◽  
Hui Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Analysis ◽  
Computational Study ◽  
Target Therapy ◽  
Janus Kinase ◽  
Dynamics Simulation ◽  
Janus Kinase 3 ◽  
Leading Compounds ◽  
Natural Inhibitors

Abstract Objective: The aim of this study is to screen and identify novel leading compounds 5 which can inhibit protein Janus Kinase 3 (JAK3) from a drug library (ZINC database) 6 to provide precise target therapy for lung cancer. 7Methods: A set of computation-aided structural biology methods and chemical virtual 8 screening techniques were carried out to screen novel inhibitor compounds. Libdock 9 scores for potential inhibitors of JAK3 were calculated using fast docking method-10 virtual screening. Next, ADMET properties (absorption, distribution, metabolism, 11 excretion, and toxicity) were conducted to predict their pharmacological characteristics. 12 The binding affinity as well as the interactions between the candidate compounds and 13 JAK3 were calculated and visualized by precise molecular docking algorithm. 14 Ultimately, molecular dynamics simulation (MD) was performed to estimate the 15 stability of the ligand-JAK3 complex under natural environment. 16Results: After screening, two novel natural compounds, ZINC000014952116 and 17 ZINC00000393864, were finally selected as leading compounds from the ZINC15 18 database, which possessed less Ames mutagenicity, rodent carcinogenicity and 19 developmental toxicity potential than other candidate compounds. Additionally, they 20 didn’t inhibit the activity of CYP2D6. Molecular dynamics simulation analysis showed 21 that ZINC000014952116 and ZINC00000393864 could interact with JAK3 steadily, 22 and their ligand-JAK3 complexes could keep stable under natural situation, and act as 23 regulatory role to JAK3. 24Conclusion: This study analyzed that ZINC000014952116 and ZINC00000393864 25 were ideal natural inhibitors targeting JAK3 from the ZINC15 database, which could 26 also provide more options and resources for other cancer chemotherapy.

scholarly journals Computational Study on Selective PDE9 Inhibitors on PDE9-Mg/Mg, PDE9-Zn/Mg, and PDE9-Zn/Zn Systems

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 709
Author(s):  
Dakshinamurthy Sivakumar ◽  
Sathish-Kumar Mudedla ◽  
Seonghun Jang ◽  
Hyunjun Kim ◽  
Hyunjin Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Erectile Dysfunction ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Cardiovascular Diseases ◽  
Neurodegenerative Disorders ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Interaction Patterns

PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibitors BAY73-6691R, BAY73-6691S, 28r, 28s, 3r, 3s, PF-0447943, PF-4181366, and 4r to elucidate the differences in their interaction patterns in the presence of different metal systems such as Zn/Mg, Mg/Mg, and Zn/Zn. The initial complexes were generated by molecular docking followed by molecular dynamics simulation for 100 ns in triplicate for each system to understand the interactions’ stability. The results were carefully analyzed, focusing on the ligands’ non-bonded interactions with PDE9 in different metal systems.

Molecular dynamics simulation analysis of conessine against multi drug resistant Serratia marcescens

2019 ◽  
Vol 67 ◽  
pp. 101-111
Author(s):  
Kalyani Dhusia ◽  
Kalpana Raja ◽  
Pierre Paul Michel Thomas ◽  
Pramod K. Yadav ◽  
Pramod W. Ramteke
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Serratia Marcescens ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Drug Resistant

scholarly journals A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11171
Author(s):  
Neha Srivastava ◽  
Prekshi Garg ◽  
Prachi Srivastava ◽  
Prahlad Kishore Seth
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Site ◽  
Cinnamic Acid ◽  
Simulation Study ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Receptor Protein ◽  
Novel Therapeutic

Background & Objectives The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. Methods In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. Results Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (−5.20 kcal/mol), thymoquinone (−4.71 kcal/mol), and andrographolide (Kalmegh) (−4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use. Interpretation & Conclusions The study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention.

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