Conceptual design of hybrid PCSK9 lead inhibitors against coronary artery disease

Puratchikody, Ayarivan; Irfan, Navabshan; Balasubramaniyan, Sakthivel

doi:10.1016/j.bcab.2018.12.014

Cited by 10 publications

(4 citation statements)

References 28 publications

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“…When the 3D structure of the protein-inhibitor complex is known, the LUDI protocol is often used to suggest new substituents for an already known inhibitor. LUDI can fit fragments into interaction sites and link them to an existing ligand at the same time [ 14 , 15 , 16 ]. LUDI generates the features that may be tedious to detect in virtual screening and other experiments, such as in ligand-based pharmacophore modeling [ 15 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Receptor-Based Pharmacophore Modeling in the Search for Natural Products for COVID-19 Mpro

2021

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Considering the urgency of the COVID-19 pandemic, we developed a receptor-based pharmacophore model for identifying FDA-approved drugs and hits from natural products. The COVID-19 main protease (Mpro) was selected for the development of the pharmacophore model. The model consisted of a hydrogen bond acceptor, donor, and hydrophobic features. These features demonstrated good corroboration with a previously reported model that was used to validate the present model, showing an RMSD value of 0.32. The virtual screening was carried out using the ZINC database. A set of 208,000 hits was extracted and filtered using the ligand pharmacophore mapping, applying the lead-like properties. Lipinski’s filter and the fit value filter were used to minimize hits to the top 2000. Simultaneous docking was carried out for 200 hits for natural drugs belonging to the FDA-approved drug database. The top 28 hits from these experiments, with promising predicted pharmacodynamic and pharmacokinetic properties, are reported here. To optimize these hits as Mpro inhibitors and potential treatment options for COVID-19, bench work investigations are needed.

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Section: Introductionmentioning

confidence: 99%

Receptor-Based Pharmacophore Modeling in the Search for Natural Products for COVID-19 Mpro

2021

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“…The MD molecule analyses 1QG6's temperature and stability. Standard dynamic cascade and minimization research protocol were utilised (Puratchikody et al, 2019).…”

Section: Mdsmentioning

confidence: 99%

Identification of Potential Inhibitor Targeting InhA, Molecular Docking, ADMET, Molecular Dynamic Simulation and Antibacterial Activity of Thiazolidinone Derivatives: A Computational Approach

P.¹,

M.²,

Santhanalakshmi³

et al. 2022

IJZI

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This study was performed to examine molecular docking of newly synthesised thiazolidinone compounds and discover potential InhA inhibitors. MIC screening produced thiazolidinone derivatives for Staphylococcus aureus illness. KBr pellet FT-IR spectra were collected on a Thermo Nicolet AVATAR-330 spectrometer. Bruker obtained 400 MHz 1H spectra of all chemicals in DMSO-d6. Five 4 thiazolidinone derivatives:4-(4-oxo-2-phenylthiazolidin-3yl)amino)benzyl)oxazolidin-2-one(8), ((2-(4 chlorophenyl)-4oxothiazolidin-3yl)amino)benzyl)- oxazolidin-2-one(9), ((2-(4-fluorophenyl)-4-oxothiazolidin-3 yl)amino)benzyl)oxazolidin-2-one(10), 4-(4-((4-oxo2-(p-tolyl)thiazolidin-3yl)amino)benzyl)oxazolidin-2-one(11) and 4-(4-((2-(4 methoxyphenyl)-4-oxothiazolidin3yl)amino)benzyl)oxazolidin-2-one(12) docked due to its vast biological usefulness. Molecular docking, ADMET, TOPKAT Toxicity, and molecular dynamic simulation were used to estimate drug-likeness for 1QG6. MIC screening of synthesised thiazolidinone derivatives against Staphylococcus aureus through disc diffusion. Molecular docking studies examining the inhibitory effect of produced substances suggest testing for MIC antibacterial activity. Compound 12's antibacterial activity against Staphylococcus aureus is compared to Ampicillin and Cefixime. Compound 12 is utilised as an alternate medication for Staphylococcus aureus

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“…Overall, ve step MDS run was conducted. The steps were followed by minimization one and two, heating, equilibration and production [57,58].…”

Section: Molecular Docking Of the Chimeric Vaccine (Eisvac) With The Immune Receptormentioning

confidence: 99%

Insilico Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium Tuberculosis H37Rv; An Immunoinformatics Approach

Radhakrishnan

Lavanya²,

Jamal

et al. 2021

Preprint

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Mycobacterium tuberculosis (Mtb) is a respiratory pathogen that causes Tuberculosis disease (TB). There are a large number of proteins that are involved in the pathogenesis of TB. Stimulating the immune response against TB is very important to clear the pathogens from host. In the present study, an Immunoinformatics conduit is used for epitope based chimeric vaccine designing against TB. Enhanced Intracellular Survival (EIS) protein from Mtb is used for designing the chimeric vaccine. 1 B-cell epitope, 8 cytotoxic T lymphocyte (CTL) and 6 Helper T lymphocyte (HTL) epitopes were predicted based on the MHC allele binding, immunogenicity, antigenicity, allergenicity, toxicity and IFN epitopes. The selected epitopes were used for chimeric vaccine designing. Further, 3D structure elucidation, structural refinement and validation of the designed chimeric vaccine was carried out. The 3D structure was used for Protein-Protein docking studies with Toll like receptor 4 (TLR-4), followed by molecular dynamic simulation (MDS) and the interaction between the chimeric vaccine and TLR-4 complex was verified.

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Conceptual design of hybrid PCSK9 lead inhibitors against coronary artery disease

Cited by 10 publications

References 28 publications

Receptor-Based Pharmacophore Modeling in the Search for Natural Products for COVID-19 Mpro

Receptor-Based Pharmacophore Modeling in the Search for Natural Products for COVID-19 Mpro

Identification of Potential Inhibitor Targeting InhA, Molecular Docking, ADMET, Molecular Dynamic Simulation and Antibacterial Activity of Thiazolidinone Derivatives: A Computational Approach

Insilico Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium Tuberculosis H37Rv; An Immunoinformatics Approach

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