An in silico approach to discover the best molecular modeling strategy for designing novelCDK4 inhibitors

2019 ◽  
Vol 93 (4) ◽  
pp. 556-569 ◽  
Author(s):  
Divya Vasanthakumari ◽  
Pushpa Vadakkethil Lalithabhai ◽  
Manoj Kanthimathi Bahuleyan
Keyword(s):  
Molecular Modeling ◽  
In Silico ◽  
Modeling Strategy

In Silico Identification of Novel APRIL Peptide Antagonists and Binding Insights by Molecular Modeling and Immunosorbent Assays

2015 ◽  
Vol 22 (5) ◽  
pp. 432-442 ◽  
Author(s):  
Joao Silva ◽  
Flavia Calmon-Hamaty ◽  
Wilson Savino ◽  
Michael Hahne ◽  
Ernesto Caffarena
Keyword(s):  
Molecular Modeling ◽  
In Silico ◽  
Immunosorbent Assays

Coumarinyl Aryl/Alkyl Sulfonates with Dual Potential: Alkaline Phosphatase and ROS Inhibitory Activities: In-Silico Molecular Modeling and ADME Evaluation

2019 ◽  
Vol 16 (3) ◽  
pp. 256-272
Author(s):  
Uzma Salar ◽  
Khalid Mohammed Khan ◽  
Syeda Abida Ejaz ◽  
Abdul Hameed ◽  
Mariya al-Rashida ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Alkaline Phosphatase ◽  
Molecular Modeling ◽  
In Silico ◽  
Smooth Muscles ◽  
Reactive Oxygen ◽  
Oxygen Species ◽  
Selective Inhibitors ◽  
Specific Alkaline Phosphatase ◽  
Inhibitory Activities

Background: Alkaline Phosphatase (AP) is a physiologically important metalloenzyme that belongs to a large family of ectonucleotidase enzymes. Over-expression of tissue non-specific alkaline phosphatase has been linked with ectopic calcification including vascular and aortic calcification. In Vascular Smooth Muscles Cells (VSMCs), the high level of Reactive Oxygen Species (ROS) resulted in the up-regulation of TNAP. Accordingly, there is a need to identify highly potent and selective inhibitors of APs for treatment of disorders related to hyper activity of APs. </P><P> Methods: Herein, a series of coumarinyl alkyl/aryl sulfonates (1-40) with known Reactive Oxygen Species (ROS) inhibition activity, was evaluated for alkaline phosphatase inhibition against human Tissue Non-specific Alkaline Phosphatase (hTNAP) and Intestinal Alkaline Phosphatase (hIAP). </P><P> Results: With the exception of only two compounds, all other compounds in the series exhibited excellent AP inhibition. For hIAP and hTNAP inhibition, IC50 values were observed in the range 0.62-23.5 &#181;M, and 0.51-21.5 &#181;M, respectively. Levamisole (IC50 = 20.21 &#177; 1.9 &#181;M) and Lphenylalanine (IC50 = 100.1 &#177; 3.15 &#181;M) were used as standards for hIAP and hTNAP inhibitory activities, respectively. 4-Substituted coumarinyl sulfonate derivative 23 (IC50 = 0.62 &#177; 0.02 &#181;M) was found to be the most potent hIAP inhibitor. Another 4-substituted coumarinyl sulfonate derivative 16 (IC50 = 0.51 &#177; 0.03 &#181;M) was found to be the most active hTNAP inhibitor. Some of the compounds were also found to be highly selective inhibitors of APs. Detailed Structure-Activity Relationship (SAR) and Structure-Selectivity Relationship (SSR) analysis were carried out to identify structural elements necessary for efficient and selective AP inhibition. Molecular modeling and docking studies were carried out to rationalize the most probable binding site interactions of the inhibitors with the AP enzymes. In order to evaluate drug-likeness of compounds, in silico ADMETox evaluation was carried out, most of the compounds were found to have favorable ADME profiles with good predicted oral bioavailability. X-ray crystal structures of compounds 38 and 39 were also determined. </P><P> Conclusion: Compounds from this series may serve as lead candidates for future research in order to design even more potent, and selective inhibitors of APs.

Molecular Modeling Studies on 2,4-Disubstituted Imidazopyridines as Anti-Malarials: Atom-Based 3D-QSAR, Molecular Docking, Virtual Screening, In-Silico ADMET and Theoretical Analysis

2021 ◽  
pp. 2150012
Author(s):  
Suraj N. Mali ◽  
Anima Pandey
Keyword(s):  
Molecular Docking ◽  
Molecular Modeling ◽  
Virtual Screening ◽  
In Silico ◽  
Energy Gap ◽  
3D Qsar ◽  
Modeling Studies ◽  
In Vitro Investigation ◽  
In Silico Admet ◽  
Molecular Modeling Studies

Malarial parasites have been reported for moderate-high resistance towards classical antimalarial agents and henceforth development of newer novel chemical entities targeting multiple targets rather than targeting single target will be a highly promising strategy in antimalarial drug discovery. Herein, we carried out molecular modeling studies on 2,4-disubstituted imidazopyridines as anti-hemozoin formation inhibitors by using Schrödinger’s molecular modeling package (2020_4). We have developed statistically robust atom-based 3D-QSAR model (training set, [Formula: see text]; test set, [Formula: see text]; [Formula: see text] [Formula: see text]; root-mean-square error, [Formula: see text]; standard deviation, [Formula: see text]). Our molecular docking, in-silico ADMET analysis showed that dataset molecule 37, has highly promising results. Our ligand-based virtual screening resulted in top five ZINC hits, among them ZINC73737443 hit was observed with lesser energy gap, i.e. 7.85[Formula: see text]eV, higher softness value (0.127[Formula: see text]eV), and comparatively good docking score of [Formula: see text]10.2[Formula: see text]kcal/mol. Our in-silico analysis for a proposed hit, ZINC73737443 showed that this molecule has good ADMET, in-silico nonames toxic as well as noncarcinogenic profile. We believe that further experimental as well as the in-vitro investigation will throw more lights on the identification of ZINC73737443 as a potential antimalarial agent.

scholarly journals Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1

2013 ◽  
Vol 7 ◽  
pp. BBI.S12449 ◽  
Author(s):  
Ajit K. Sharma ◽  
Abhilasha Mansukh ◽  
Ashok Varma ◽  
Nikhil Gadewal ◽  
Sanjay Gupta
Keyword(s):  
Molecular Modeling ◽  
Protein Kinase ◽  
Chromatin Structure ◽  
In Silico ◽  
Association Studies ◽  
Regulatory Proteins ◽  
Mitogen Activated Protein Kinase ◽  
Site Specific ◽  
Mitogen Activated Protein ◽  
Neighboring Site

Histone modifications occur in precise patterns, with several modifications known to affect the binding of proteins. These interactions affect the chromatin structure, gene regulation, and cell cycle events. The dual modifications on the H3 tail, serine10 phosphorylation, and lysine14 acetylation (H3Ser10PLys14Ac) are reported to be crucial for interaction with 14-3-3ζ. However, the mechanism by which H3Ser10P along with neighboring site-specific acetylation(s) is targeted by its regulatory proteins, including kinase and phosphatase, is not fully understood. We carried out molecular modeling studies to understand the interaction of 14-3-3ζ, and its regulatory proteins, mitogen-activated protein kinase phosphatase-1 (MKP1), and mitogen- and stress-activated protein kinase-1 (MSK1) with phosphorylated H3Ser10 alone or in combination with acetylated H3Lys9 and Lys14. In silico molecular association studies suggested that acetylated Lys14 and phosphorylated Ser10 of H3 shows the highest binding affinity towards 14-3-3ζ. In addition, acetylation of H3Lys9 along with Ser10PLys14Ac favors the interaction of the phosphatase, MKP1, for dephosphorylation of H3Ser10P. Further, MAP kinase, MSK1 phosphorylates the unmodified H3Ser10 containing N-terminal tail with maximum affinity compared to the N-terminal tail with H3Lys9AcLys14Ac. The data clearly suggest that opposing enzymatic activity of MSK1 and MKP1 corroborates with non-acetylated and acetylated, H3Lys9Lys14, respectively. Our in silico data highlights that site-specific phosphorylation (H3Ser10P) and acetylation (H3Lys9 and H3Lys14) of H3 are essential for the interaction with their regulatory proteins (MKP1, MSK1, and 14-3-3ζ) and plays a major role in the regulation of chromatin structure.

scholarly journals Design of Improved Anti-Influenza Peptide Mimetics Using In Silico Molecular Modeling

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Kenneth A. Mwawasi ◽  
David C. Bulir ◽  
Seiji N. Sugiman-Manrangos ◽  
Murray S. Junop ◽  
Christopher Stone ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
In Silico ◽  
Peptide Mimetics

Synthesis, pharmacological assessment, molecular modeling and in silico studies of fused tricyclic coumarin derivatives as a new family of multifunctional anti-Alzheimer agents

2016 ◽  
Vol 107 ◽  
pp. 219-232 ◽  
Author(s):  
Jeelan Basha Shaik ◽  
Bhagath Kumar Palaka ◽  
Mohan Penumala ◽  
Kasi Viswanath Kotapati ◽  
Subba Rao Devineni ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
In Silico ◽  
Coumarin Derivatives ◽  
New Family ◽  
In Silico Studies
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