A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
Current Approaches for Investigating and Predicting Cytochrome P450 3A4-Ligand Interactions
[chapter]
2015
Advances in Experimental Medicine and Biology
Preserved Fulltext
This is possible because CYP3A4 is promiscuous with respect to substrate binding and has the ability to catalyze diverse oxidative chemistries in addition to traditional hydroxylation reactions. ...
Furthermore, CYP3A4 binds and oxidizes a number of substrates in a cooperative manner and can be both induced and inactivated by drugs. ...
Acknowledgments Financial support from the National Institute of General Medical Sciences (Grant GM57353) and the California Center for Antiviral Drug Discovery is gratefully appreciated. ...
doi:10.1007/978-3-319-16009-2_3
pmid:26002732
pmcid:PMC4532289
fatcat:7ujdyyp3sfgwblvrl56bop3zou
Structure-Based Drug Design for Cytochrome P450 Family 1 Inhibitors
2018
Bioinorganic Chemistry and Applications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Moreover, the molecular modeling of proteins and ligand docking to their active sites provide an insight into the mechanism of enzyme action and enable us to predict the sites of drug metabolism. ...
The review presents the current status of knowledge about the use of the computational approach in studies of ligand-enzyme interactions for CYP1s. ...
Docking may be used to provide information about the conformation of a bioactive ligand and its position in the binding site. ...
doi:10.1155/2018/3924608
pmid:30147715
pmcid:PMC6083639
fatcat:5hdcm4kyo5bd5aqqdhkjy3hpgi
Identifying the alpha-glucosidase inhibitory potential of dietary phytochemicals against diabetes mellitus type 2 via molecular interactions and dynamics simulation
2022
Cellular and Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Molecular dynamics simulation of 10 ns duration, CYP450 site of metabolism identification, and prediction of activity spectra for substances depicted the bromelain as the most stable inhibitor compared ...
alpha-glucosidase in comparison to the best-known inhibitor, acarbose (ΔG: -7.93 kcal/mol). ...
Interest conflict The authors declare no conflict of interest. ...
doi:10.14715/cmb/2021.67.5.3
fatcat:gaaxewiqgzghnfvn4cuihprweu
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
2020
Processes
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate ...
In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields ...
Their other study on the conformational changes of the SIRT2 substrate and inhibitor binding sites revealed the dynamic role of Phe96 in binding the inhibitor in SIRT2 [81] . ...
doi:10.3390/pr9010071
fatcat:x6pcyzoxevbvhncirfrkqiuppq
In Silico Prediction, Molecular Docking and Dynamics Studies of Steroidal Alkaloids of Holarrhena pubescens Wall. ex G. Don to Guanylyl Cyclase C: Implications in Designing of Novel Antidiarrheal Therapeutic Strategies
2021
Molecules
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
We carried out this study with the objective of finding ligands that would interfere with the binding of STa on ECDGC-C. ...
This suggests that holadysenterine has the potential to inhibit binding of STa on ECD and can be considered for future study, involving its validation through in vitro assays and animal model studies. ...
Acknowledgments: We would like to acknowledge Ashok K. Chauhan, Founder President, Amity University Uttar Pradesh, Noida for providing the infrastructure and support. ...
doi:10.3390/molecules26144147
pmid:34299422
pmcid:PMC8305770
fatcat:wbpg7f6jifhjbo5qkilljmylu4
Computational Prediction of Potential Inhibitors of the Main Protease of SARS-CoV-2
2020
Frontiers in Chemistry
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
To facilitate the rapid discovery of inhibitors with clinical potential, we have applied ligand- and structure-based computational approaches to develop a virtual screening methodology that allows us to ...
Additionally, we have used an integrated drug repurposing approach to computationally identify potential inhibitors of the main protease of SARS-CoV-2 in databases of drugs (both approved and withdrawn ...
A conformational change then occurs, and the positions adopted by the ligand from 30 to 100 ns preclude contacts with binding-site residues. ...
doi:10.3389/fchem.2020.590263
pmid:33425850
pmcid:PMC7786237
fatcat:6c7dvwelxndr3dyn6tejww3hlm
Computational Methods in Drug Discovery
2013
Pharmacological Reviews
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
Authorship Contributions Wrote or contributed to the writing of the manuscript: Sliwoski, Kothiwale, Meiler, Lowe. ...
Desolvation of ligand and binding pocket, shifts in the ligand and protein conformational ensembles, and reordering of water molecules in the binding site all contribute to binding free energies. ...
Structural insight of binding site allowed the investigators to apply ligands containing an N-(2adamantyl) amide moiety in a drug design program. ...
doi:10.1124/pr.112.007336
pmid:24381236
pmcid:PMC3880464
fatcat:4dzrdkspkjecnombnchznma2ny
Molecular Docking and Dynamic Simulation of AZD3293 and Solanezumab Effects Against BACE1 to Treat Alzheimer's Disease
2018
Frontiers in Computational Neuroscience
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
The design of novel inhibitors to target BACE1 with reduced cytotoxicity effects is a promising approach to treat Alzheimer's disease (AD). ...
The molecular docking results show that AZD3293 binds within the active region of BACE1 by forming hydrogen bonds against Asp32 and Lys107 with distances 2.95 and 2.68 Å, respectively. ...
In the future, a molecular dynamics simulation study may be used as good computational approach to study the interactions of Aβ40 and Aβ42 with model neuronal membranes. ...
doi:10.3389/fncom.2018.00034
pmid:29910719
pmcid:PMC5992503
fatcat:df3qd4z7fnhbrdvraspthdruhq
Molecular Basis of Metabolism-Mediated Conversion of PK11195 from an Antagonist to an Agonist of the Constitutive Androstane Receptor
2017
Molecular Pharmacology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We show that although PK11195 antagonizes hCAR in HepG2 cells, it induces the expression of CYP2B6 and CYP3A4, targets of hCAR and the pregnane X receptor (PXR), in HPH, HepaRG, and PXR-knockout HepaRG ...
Here, we investigated the effects of PK11195 on hCAR in metabolically competent human primary hepatocytes (HPH) and HepaRG cells. ...
The LC-MS analysis of PK11195 metabolism was performed in the Mass Spectrometry Center at the University of Maryland School of Pharmacy. ...
doi:10.1124/mol.117.108621
pmid:28442602
pmcid:PMC5452073
fatcat:ndlbq7huhnfzngzo6tarcyy7vy
The 18th European Symposium on Quantitative Structure–Activity Relationships
2011
Expert Opinion on Drug Discovery
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
effective binding in the kinase. ...
Furthermore, the conducted docking studies elucidated the possible alternative binding mode of the ligands into the ATP binding cleft and assigned their physicochemical and structural features which promote ...
Several different binding modes were produced due to the conformational flexibility of the small ligands compared to the dimensions of the active site. ...
doi:10.1517/17460441.2011.560604
pmid:22646021
fatcat:tb4bhvtnpzahxm4xba7iw4afuy
Potential Therapeutic Candidates against Chlamydia pneumonia Discovered and Developed In Silico Using Core Proteomics and Molecular Docking and Simulation-Based Approaches
2022
International Journal of Environmental Research and Public Health
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Molecular docking experiments were also evaluated using molecular dynamics simulations and the widely used MM-GBSA and MM-PBSA binding free energy techniques. ...
In the present study, an approach named subtractive proteomics was employed to the core proteomes of five strains of C. pneumonia using various bioinformatic tools, servers, and software. ...
Acknowledgments: The authors extend their appreciation to Taif University for funding the current work by Taif University Researchers Supporting Project number (TURSP-2020/59), Taif University, Taif, Saudi ...
doi:10.3390/ijerph19127306
pmid:35742569
fatcat:h772mre4xvhndlg3powxpebwae
Identification of FDA Approved Drugs Against SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) and 3-chymotrypsin-like Protease (3CLpro), Drug Repurposing Approach
2021
Biomedicine and Pharmacotherapy
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Six drugs based on binding energy and number of hydrogen bonds were chosen for the next step of molecular dynamics (MD) simulations to investigate drug-protein interactions (including Nilotinib, Imatinib ...
In this study, FDA-approved drugs were screened to identify the probable anti-RdRp and 3CLpro inhibitors by molecular docking approach. ...
Acknowledgments The authors thank the Proteomics Research Center of Shahid Beheshti University of Medical Sciences for their support in conducting this work (NO. 22784). ...
doi:10.1016/j.biopha.2021.111544
fatcat:aky3xdqbczbg5l4tt76i6dm754
Tripeptides from Allium subhirsitum L. extracts: Pharmacokinetics properties, toxicity prediction and in silico study against SARS-CoV-2 enzymes and pro-inflammatory proteins
2022
Cellular and Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
The obtained promising results showed that the peptides (Asn-Asn-Asn) possess the highest binding affinities of -8.4 kcal/mol against S protein, (His-Phe-Gln) of -9.8 kcal/mol and (Gln-His-Phe) of -9.7 ...
Since no available clinically antiviral drugs have been approved to eradicate COVID-19 as of the writing of this report, this study aimed to investigate bioactive short peptides from Allium subhirsutum ...
Structure-based virtual screening is applied to identify the best binding conformation of the ligands within the receptor binding site. ...
doi:10.14715/cmb/2021.67.4.17
fatcat:sfiduqjuxvesvocbkmipawdiqy
Computational approach towards the design of artemisinin–thymoquinone hybrids against main protease of SARS-COV-2
2021
Future Journal of Pharmaceutical Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
inhibitors, low risk of toxicity compared to commercially available drugs, considering mainly mutagenicity and cardiotoxicity, low capacity of hybrids to permeate the blood–brain barrier, high absorption ...
In addition, T1–T7 tend to have a better distribution of their available fractions to carry out diffusion and transport across cell membranes, as well as increase the energy of interaction with the SARS-CoV ...
Acknowledgements The authors thank FUNCAP, CAPES and CNPq for financial support and scholarship. ...
doi:10.1186/s43094-021-00334-z
pmid:34514004
pmcid:PMC8419828
fatcat:no62b5m7rjandbtwhbddw4sbou
Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments
2021
Current Issues in Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Additionally, the in silico mutational study was carried out to understand the increase in therapeutic efficiency using site-directed mutagenesis. ...
Yohimbine was investigated in this study to determine its antidepressant activity using molecular docking and pharmacokinetic analyses. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/cimb43030127
pmid:34889886
fatcat:uvkeviga4vgtjkqjdr52jnpiei
« Previous
Showing results 1 — 15 out of 188 results