Deciphering Saquinavir-Bovine Serum Albumin Interactions: Spectroscopic and Computational Insights.

Bovine serum albumin (BSA) plays a crucial role as a carrier protein in plasma, binding various ligands, including drugs. Understanding the interaction between BSA and saquinavir, an antiretroviral drug, is essential for predicting its pharmacokinetics and pharmacodynamics. We employed spectroscopic approaches, including circular dichroism spectrometry and fluorescence spectroscopy, to investigate the binding of saquinavir to BSA.

Crystal structure and Hirshfeld surface analysis of ()--(2-styrylphen-yl)benzene-sulfonamide.

The crystal structure of the title compound CHNOS features hydrogen-bonding and C-H⋯π inter-actions. Hirshfeld surface analysis revealed that H⋯H, C⋯H/H⋯C and O⋯H/H⋯O inter-actions make a major contribution to the crystal packing. Docking studies were carried out to determine the binding affinity and inter-action profile of the title compound with EGFR kinase, a member of the ErbB family of receptor tyrosine kinases, which is crucial for processes such as cell proliferation and differentiation.

and immunoinformatics based multiepitope subunit vaccine design for protection against visceral leishmaniasis.

Visceral leishmaniasis (VL) is a vector-borne neglected tropical protozoan disease with high fatality and no certified vaccine. Conventional vaccine preparation is challenging and tedious. Here in this work, we created a global multiepitope subunit vaccination against VL utilizing innovative immunoinformatics technique based on the extensively conserved epitopic regions of the PrimPol protein of consisting of four subunits which were analyzed and studied, out of which DNA primase large subunit and DNA polymerase α subunit B were evaluated as antigens by Vaxijen 2.

Identification of the Seaweed Metabolites as Potential Anti-tubercular Agents Against Human Pantothenate synthetase: An In Silico Approach.

Tuberculosis is the disease which is caused due to the contagion of Mycobacterium tuberculosis. The multidrug resistance Mycobacterium tuberculosis is the main hassle in the treatment of this worldwide health threats. Pantothenate synthase is a legitimate goal for rational drug designing against Mycobacterium tuberculosis.

Toxicity, Pharmacokinetic Profile, and Compound-Protein Interaction Study of Polygonum minus Huds Extract.

Several phytochemicals with potential for bioactivity can be found in Polygonum minus (PM). The goal of this investigation was to establish the minimally toxic dose of PM for pharmaceutical use. To explain the stability and reactivity of the compounds under study, the lowest unoccupied molecular orbital (LUMO), the highest occupied molecular orbital (HOMO), and the natural bond orbital were all combined.

Polygenic score for Alzheimer's disease identifies differential atrophy in hippocampal subfield volumes.

Hippocampal subfield atrophy is a prime structural change in the brain, associated with cognitive aging and neurodegenerative diseases such as Alzheimer's disease. Recent developments in genome-wide association studies (GWAS) have identified genetic loci that characterize the risk of hippocampal volume loss based on the processes of normal and abnormal aging. Polygenic risk scores are the genetic proxies mimicking the genetic role of the pre-existing vulnerabilities of the underlying mechanisms influencing these changes.

In-silico studies on Myo inositol-1-phosphate synthase of in search of anti-leishmaniasis.

Myo-inositol is one of the vital nutritional requirements for the parasites' survival and virulence in the mammalian host. . Myo-inositol-1-phosphate synthase (MIPS) is responsible for the synthesis of myo-inositol in , which plays a vital role in virulence to mammalian hosts.

Insights of structure-based pharmacophore studies and inhibitor design against Gal3 receptor through molecular dynamics simulations.

Our present work studies the structure-based pharmacophore modeling and designing inhibitor against Gal3 receptor through molecular dynamics (MD) simulations extensively. Pharmacophore models play a key role in computer-aided drug discovery like in the case of virtual screening of chemical databases, drug design and lead optimization. Structure-based methods for developing pharmacophore models are important, and there have been a number of studies combining such methods with the use of MD simulations to model protein's flexibility.

Berberine and Emodin abrogates breast cancer growth and facilitates apoptosis through inactivation of SIK3-induced mTOR and Akt signaling pathway.

Salt-inducible kinases 3 (SIK3) belong to the AMPK-related family of kinases, which have been implicated in the regulation of cell metabolism, cell polarity remodelling, and epithelial-mesenchymal transition. Elevated SIK3 expressions in breast cancer cells are shown to contribute to tumorigenesis; however, the underlying mechanism remains to be elucidated. In this study, we demonstrate that SIK3 expression is upregulated and concurrently high expression of SIK3 is associated with poor survival in breast cancer.

Evaluation of potential drugs against leishmaniasis targeting catalytic subunit of nuclear DNA primase using ligand based virtual screening, docking and molecular dynamics approaches.

, causes leishmaniasis, a global health trouble with around 89 different countries and its population under its risk. Replication initiation events have been instrumental in regulating the DNA duplication and as the small subunit of nuclear DNA primase (-PriS) inherits the catalytic site, it plays a vital role in DNA replication. In this study we have aimed PriS for the first time as a prospective target for the application of drug against parasite.

Application of docking and active site analysis for enzyme linked biodegradation of textile dyes.

Growth of textile industries led to production of enormous dye varieties. These textile dyes are largely used, chemically stable and easy to synthesize. But they are recalcitrant and persist as less biodegradable pollutants when discharged into waterbodies.

Structural insights into the Aedes aegypti aquaporins and aquaglyceroporins - an in silico study.

There has been a fair bit of understanding on the structure-function relationship of Aquaporins (AQPs) from plants and vertebrates obtained from available X-ray crystallography data. However, there is a lacuna in understanding the structure of AQPs from sanguinivorous insects like the mosquito where it plays a crucial role in survival. In this study, we have built homology models for the Aedes aegypti AQPs, identified key channel lining residues and compared the structure and sequence with orthodox AQPs.

The nociceptin receptor (NOPR) and its interaction with clinically important agonist molecules: a membrane molecular dynamics simulation study.

The nociceptin receptor (NOPR) is an orphan G protein-coupled receptor that contains seven transmembrane helices. NOPR has a distinct mechanism of activation, though it shares a significant homology with other opioid receptors. Previously there have been reports on homology modeling of NOPR and also molecular dynamics simulation studies for a short period.

In silico study of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanones derivatives as CCR1 antagonist: homology modeling, docking and 3D-QSAR approach.

C-C chemokine receptor type 1 (CCR1) is a chemokine receptor with seven transmembrane helices and it belongs to the G-Protein Coupled receptor (GPCR) family. It plays an important role in rheumatoid arthritis, organ transplant rejection, Alzheimer's disease and also causes inflammation. Because of its role in disease processes, CCR1 is considered to be an important drug target.

In silico study on indole derivatives as anti HIV-1 agents: a combined docking, molecular dynamics and 3D-QSAR study.

The HIV-1 envelope glycoprotein gp120 plays a vital role in the entry of virus into the host cells and is a potential antiviral drug target. Recently, indole derivatives have been reported to inhibit HIV-1 through binding to gp120, and this prevents gp120 and CD4 interaction to inhibit the infectivity of HIV-1. In this work, molecular docking, molecular dynamics (MD) and three-dimensional quantitative structure-activity relationship studies were carried out.

Molecular insights on TNKS1/TNKS2 and inhibitor-IWR1 interactions.

Tankyrases (TNKS) belong to the poly(ADP-ribose)polymerase (PARP) protein super family and play a vital role in the Wnt/β-catenin signaling pathway. TNKS is a potential target for therapeutic intervention against various cancers, heritable diseases (e.g.

In silico study of desmosdumotin as an anticancer agent: homology modeling, docking and molecular dynamics simulation approach.

P-glycoprotein (P-gp) is responsible for the multidrug resistance (MDR) and involved in the expulsion of xenobiotics out of cell. In this paper, homology modeling, docking and molecular dynamics simulation (MDS) was performed for the human P-gp desmosdumotin inhibitor. Docking study was carried out in the P-gp nucleotide binding domain 2 (NBD2).

Theoretical characterization of galanin receptor type 3 (Gal3 ) and its interaction with agonist (GALANIN) and antagonists (SNAP 37889 and SNAP 398299): an in silico analysis.

In this study, we report on modeling of galanin receptor type 3 and its interaction with agonist and antagonists using in silico methodologies. Comparative structural modeling of galanin receptor type 3 was based on multiple templates. With the availability of reported selective galanin receptor type 3 antagonists, docking was carried out into the predicted binding site.

Binding site exploration of CCR5 using in silico methodologies: a 3D-QSAR approach.

Chemokine receptor 5 (CCR5) is an important receptor used by human immunodeficiency virus type 1 (HIV-1) to gain viral entry into host cell. In this study, we used a combined approach of comparative modeling, molecular docking, and three dimensional quantitative structure activity relationship (3D-QSAR) analyses to elucidate detailed interaction of CCR5 with their inhibitors. Docking study of the most potent inhibitor from a series of compounds was done to derive the bioactive conformation.

Computational modeling of human coreceptor CCR5 antagonist as a HIV-1 entry inhibitor: using an integrated homology modeling, docking, and membrane molecular dynamics simulation analysis approach.

Chemokine receptor 5 (CCR5) is an integral membrane protein that is utilized during human immunodeficiency virus type-1 entry into host cells. CCR5 is a G-protein coupled receptor that contains seven transmembrane (TM) helices. However, the crystal structure of CCR5 has not been reported.

Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study.

Chemokine receptors are G protein-coupled receptors that contain seven transmembrane domains. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, and furthermore, targeting both CCR2 and CCR5 can be a useful strategy.

Docking and 3D-QSAR (quantitative structure activity relationship) studies of flavones, the potent inhibitors of p-glycoprotein targeting the nucleotide binding domain.

In order to explore the interactions between flavones and P-gp, in silico methodologies such as docking and 3D-QSAR were performed. CoMFA and CoMSIA analyses were done using ligand based and receptor guided alignment schemes. Validation statistics include leave-one-out cross-validated R(2) (q(2)), internal prediction parameter by progressive scrambling (Q(*2)), external prediction with test set.