Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spectroscopic, Thermodynamic and Molecular Docking Studies on Molecular Mechanisms of Drug Binding to Proteins.

ABSTRACT: Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms [...].

SUBMITTER: Wani TA

PROVIDER: S-EPMC9738057 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Spectroscopic, Thermodynamic and Molecular Docking Studies on Molecular Mechanisms of Drug Binding to Proteins.

Wani Tanveer A TA Zargar Seema S Hussain Afzal A

Molecules (Basel, Switzerland) 20221201 23

Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms [...]. ...[more]

PMID: 36500497

Similar Datasets

Spectroscopic, thermodynamic and molecular docking studies of bovine serum albumin interaction with ascorbyl palmitate food additive.

Project description:Introduction: Ascorbyl palmitate (AP) is an example of natural secondary food antioxidant, which has been used for oxidative rancidity prevention in food industry. In this study, the interaction of AP with bovine serum albumin (BSA) was investigated. Methods: The mechanism of BSA interaction with AP was investigated using spectroscopic methods (UV-Vis, fluorescence). The thermodynamic parameters including enthalpy change (ΔH), entropy change (ΔS), and Gibb's free energy (ΔG) were calculated using Van't Hoff equation at different temperatures. Results: The experimental results showed that UV-Vis absorption spectra of BSA decreased upon increasing AP concentration, indicating that the AP can bind to BSA. Formation of the AP-BSA complex was approved by quenching of fluorescence and the quenching mechanism was found to be resultant from dynamic procedure. The positive values of both ΔH and ΔS showed that hydrophobic forces were the major binding forces. The negative value of ΔG demonstrated that AP interacts with BSA spontaneously. Molecular docking results confirmed that AP binds to BSA through hydrophobic forces. Conclusion: The attained results showed that AP can bind to BSA and effectively distributed into the bloodstream.

| S-EPMC5801535 | biostudies-literature

Study of Amiloride Binding to Human Serum Albumin: Insights from Thermodynamic, Spectroscopic, and Molecular Docking Investigations.

Project description:This study was undertaken to investigate the interaction between the sodium channel blocker amiloride (AML) and human serum albumin (HSA). A combination of multi-spectroscopic techniques and computational methods were employed to identify the AML binding site on HSA and the forces responsible for the formation of the HSA-AML complex. Our findings revealed that AML specifically binds to Sudlow's site II, located in subdomain IIIA of HSA, and that the complex formed is stabilized using van der Waals hydrogen-bonding and hydrophobic interactions. FRET analysis showed that the distance between AML and Trp214 was optimal for efficient quenching. UV-Vis spectroscopy and circular dichroism indicated minor changes in the structure of HSA after AML binding, and molecular dynamics simulations (MDS) conducted over 100 ns provided additional evidence of stable HSA-AML-complex formation. This study enhances understanding of the interaction between AML and HSA and the mechanism responsible.

| S-EPMC10707572 | biostudies-literature

Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies.

Project description:Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.

| S-EPMC7859944 | biostudies-literature

Spectroscopic and molecular docking studies reveal binding characteristics of nazartinib (EGF816) to human serum albumin.

Project description:The interactions of novel anti-cancer therapeutic agents with the different plasma and tissue components, specifically serum albumins, have lately gained considerable attention due to the significant influence of such interactions on the pharmacokinetics and/or -dynamics of this important class of therapeutics. Nazartinib (EGF 816; NAZ) is a new anti-cancer candidate proposed as a third-generation epidermal growth factor receptor tyrosine kinase inhibitor that is being developed and clinically tested for the management of non-small cell lung cancer. The current study aimed to characterize the interaction between NAZ and human serum albumin (HSA) using experimental and theoretical approaches. Experimental results of fluorescence quenching of HSA induced by NAZ revealed the development of a statically formed complex between NAZ and HSA. Interpretation of the observed fluorescence data using Stern-Volmer, Lineweaver-Burk and double-log formulae resulted in binding constants for HSA-NAZ complex in the range of (2.34-2.81) × 104 M-1 over the studied temperatures. These computed values were further used to elucidate thermodynamic attributes of the interaction, which showed that NAZ spontaneously binds to HSA with a postulated electrostatic force-driven interaction. This was further verified by theoretical examination of the NAZ docking on the HSA surface that revealed an HSA-NAZ complex where NAZ is bound to HSA Sudlow site I driven by hydrogen bonding in addition to electrostatic forces in the form of pi-H bond. The HSA binding pocket for NAZ was shown to encompass ARG 257, ARG 222, LYS 199 and GLU 292 with a total binding energy of -25.59 kJ mol-1.

| S-EPMC7029911 | biostudies-literature

Spectroscopic and molecular docking studies on binding interactions of camptothecin drugs with bovine serum albumin.

Project description:This study investigates the binding interactions between bovine serum albumin (BSA) and camptothecin (CPT) drugs (camptothecin, 10-hydroxycamptothecin, topotecan, and irinotecan) using UV-Vis spectroscopy, fluorescence spectroscopy, three-dimensional fluorescence spectroscopy, and molecular docking techniques. The fluorescence quenching of BSA by CPT drugs follows a static mechanism, with binding constants (Kb) ranging from 4.23 × 103 M- 1 (CPT) to 101.30 × 103 M- 1 (irinotecan), demonstrating significant drug binding selectivity. Thermodynamic analysis reveals distinct interaction mechanisms: topotecan binding is driven by hydrogen bonding (ΔH = - 10.96 kJ·mol- 1) and hydrophobic interactions (ΔS = 0.066 kJ·mol- 1·K- 1), while irinotecan exhibits stronger binding dominated by electrostatic forces (ΔH = - 86.77 kJ·mol- 1) with significant entropy loss (ΔS = - 0.161 kJ·mol- 1·K- 1). Molecular docking confirms preferential binding at Sudlow site I of BSA, with hydrophobic interactions and hydrogen bonding as the primary driving forces. These findings provide a comprehensive understanding of CPT-BSA interactions, offering valuable insights for the design of albumin-based drug delivery systems with optimized pharmacokinetic profiles.

| S-EPMC11889159 | biostudies-literature

Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib.

Project description:Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV-Vis spectrophotometry, and viscosity assessment. The binding constant (Kb) at 298 K calculated from the Benesi-Hildebrand equation was found to be 6.42 × 103 M-1. The enthalpy and entropy changes (∆H0 and ∆S0) were - 33.09 kJ mol-1 and 61.78 J mol-1 K-1, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.

| S-EPMC9427788 | biostudies-literature

Electrochemical, spectroscopic, and molecular docking studies of the interaction between the anti-retroviral drug indinavir and dsDNA.

Project description:In this study, an electrochemical DNA biosensor was developed using a straightforward methodology to investigate the interaction of indinavir with calf thymus double-stranded deoxyribonucleic acid (ct-dsDNA) for the first time. The decrease in the oxidation signals of deoxyguanosine (dGuo) and deoxyadenosine (dAdo), measured by differential pulse voltammetry, upon incubation with different concentrations of indinavir can be attributed to the binding mode of indinavir to ct-dsDNA. The currents of the dGuo and dAdo peaks decreased linearly with the concentration of indinavir in the range of 1.0-10.0 μg/mL. The limit of detection and limit of quantification for indinavir were 0.29 and 0.98 μg/mL, respectively, based on the dGuo signal, and 0.23 and 0.78 μg/mL, respectively, based on the dAdo signal. To gain further insights into the interaction mechanism between indinavir and ct-dsDNA, spectroscopic measurements and molecular docking simulations were performed. The binding constant (Kb) between indinavir and ct-dsDNA was calculated to be 1.64 × 108 M-1, based on spectrofluorometric measurements. The obtained results can offer insights into the inhibitory activity of indinavir, which could help to broaden its applications. That is, indinavir can be used to inhibit other mechanisms and/or hallmarks of viral diseases.

| S-EPMC7591812 | biostudies-literature

Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques.

Project description:Eltrombopag is a powerful adjuvant anticancer drug used in treating MS (myelodysplastic syndrome) and AML (acute myeloid leukemia) diseases. In this study, the interaction mechanism between eltrombopag and DNA was studied by voltammetry, spectroscopic techniques, and viscosity measurements. We developed a DNA-based biosensor and nano-biosensor using reduced graphene oxide-modified glassy carbon electrode to detect DNA-eltrombopag binding. The reduction of desoxyguanosine (dGuo) and desoxyadenosine (dAdo) oxidation signals in the presence of the drug demonstrated that a strong interaction could be established between the eltrombopag and dsDNA. The eltrombopag-DNA interaction was further investigated by UV absorption and fluorescence emission spectroscopy to gain more quantitative insight on binding. Viscosity measurements were utilized to characterize the binding mode of the drug. To shed light on the noncovalent interactions and binding mechanism of eltrombopag molecular docking and molecular dynamics (MD), simulations were performed. Through simultaneously carried out experimental and in silico studies, it was established that the eltrombopag binds onto the DNA via intercalation.

| S-EPMC10046231 | biostudies-literature

Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor.

Project description:Quercitrin is an anti-lung cancer agent. It is a naturally occurring flavonoid and its derivatives are mainly present in nuts and beverages. It is mainly available as a glycoside, and the quercitrin glycosides are found to prevent the metastasis of cancer. Quercitrin is optimized with 6-311++G(d,p) basis set using the B3LYP method to attain its minimum energy structure. The vibrational studies of the Quercitrin compound were elucidated with reference to Potential Energy Distribution (PED). The geometrical parameters were obtained and correlated with experimental values. To examine the nature of the charge transfer mechanism of Quercitrin, the HOMO-LUMO energy gap is computed. The anti-cancer activity of Quercitrin has been explored using molecular docking study that are used to estimate how the ligand interacts with protein, specifically to identify the best-fit orientation of the ligand, its binding mode, and intermolecular interactions of amino acid residues in the binding region of B-RAF kinase protein. The binding affinity of the compound Quercitrin (-7.14 kcal/mol) was found using AutoDock and validated with a Glide XP score in Schrodinger tool (-8.01 kcal/mol). MD simulations of protein-ligand complexes were monitored for 100 ns, from which the RMSD, RMSF, Rg, H-bonds, and interaction energy calculations were executed. From these investigations, it is identified that the compound quercitrin has maintained good structural stability, compactness, higher Hydrogen bonds, and interaction energies than the Imidazopyridinyl benzamide inhibitor.

| S-EPMC9160043 | biostudies-literature

Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.

Project description:A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.

| S-EPMC3460968 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data