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Simulation at Atomic Scale
Published in Chinmay K. Maiti, Fabless Semiconductor Manufacturing, 2023
A molecule is a stable arrangement of a group of nuclei and electrons. The exact arrangement can be described by electromagnetic force and quantum mechanical laws. Another picture of a molecule as a stable structure formed by the association of two or more atoms. In this case, the atoms retain their identity, whereas in the first case it is not. When a molecule is formed by using two atoms, the inner shell electron of each atom may be tightly bound to the nucleus or barely distributed. The outermost loosely bound electrons are known as valance electrons, are influenced by particles. The wave function is significantly modified when the atoms are brought together. The interatomic force is the electromagnetic interaction; hence the valance electron plays the important role in molecular binding. There are two main types of molecular binding, i.e., the ionic bond and the covalent bond. NaCl is a molecule held together by an ionic bond, whereas binding in an H2 molecule is a covalent bond having the energy of the Coulombic interaction of ions.
Cloud Application in Drug Development
Published in Rishabha Malviya, Pramod Kumar Sharma, Sonali Sundram, Rajesh Kumar Dhanaraj, Balamurugan Balusamy, Bioinformatics Tools and Big Data Analytics for Patient Care, 2023
Nitu Singh, Urvashi Sharma, Deepika Bairagee, Neelam Jain
For medications that target specific biological molecules, a high enough binding affinity between the drug and its target is required for the drug’s potency to develop. As a result, throughout the drug development stages of hit identification, lead generation (hit to lead), and optimisation, binding affinity is one of the most important optimisation targets. A group of compounds with verified action to the biological target is identified for hit identification via high throughput screening or virtual screening, followed by experimental validation from a library of varied compounds. Because of its consistent accuracy and efficiency, FEP has gained traction as a computational tool for predicting binding affinities between candidate drugs and their biological targets. To move the system from one real ligand to another (the relative binding free energy approach, RBFE) or from the target-ligand complex to the separated target and ligand state, FEP uses a sequence of well-defined alchemical states (the absolute binding free energy method, ABFE).
Product Quality and Process
Published in Wei-Shou Hu, Cell Culture Bioprocess Engineering, 2020
Since mAbs are the largest class of therapeutic proteins, binding assays between an antigen and an antibody are a commonly practiced functional assay. The binding kinetics are measured by surface plasmon resonance (SPR) (Figure 4.7). First, the ligand proteins are immobilized onto the sensor chip. The antibody protein is then flowed into the ligand-coated binding reaction chamber to allow for the measurement of antibody association to the ligand. This is followed by a period of dissociation in which a solution without the antibody is flowed through to measure the kinetics of dissociation. The process is repeated after regeneration of the surface immobilization of the ligand. The surface resonance increases as antibodies and ligands form complexes in the association phase and decreases in the dissociation phase. Using the binding kinetic equations, the rate constant of binding and dissociation can be determined.
Investigation on the interaction of food colorant Sudan III with bovine serum albumin using spectroscopic and molecular docking methods
Published in Journal of Environmental Science and Health, Part A, 2020
Jie Bai, Xiping Ma, Xuekai Sun
There are four types of binding forces between biological macromolecules and small organic molecules: (1) hydrogen bonds; (2) van der Waals’ interactions; (3) electrostatic forces; and (4) hydrophobic interactions. The enthalpy change can be regarded as a constant when the temperature does not vary significantly.[25] To elucidate the binding forces between Sudan III and BSA, the thermodynamic parameters, enthalpy change (ΔH), free energy (ΔG), and entropy change (ΔS) are calculated from the van’t Hoff Eqs. (4)–(6):[26] where R is the gas constant, T is the temperature, and K is the binding constants at the corresponding temperature. Table 1 gives the thermodynamic parameters for the interaction of Sudan III with BSA. The negative sign for ΔG means that the interaction between Sudan III to BSA is spontaneous. The positive values of ΔS and negative value of ΔH reveal that van der Waals forces and hydrogen bonds are primarily involved in stabilizing the Sudan III–BSA complex.[27]
Antiproliferative activity and human serum albumin binding propensity of [SnMe2Cl2(bu2bpy)]: multi-spectroscopic analysis, atomic force microscopy, and computational studies
Published in Journal of Coordination Chemistry, 2020
Nahid Shahabadi, Saba Zendehcheshm, Badri Z Momeni, Reyhaneh Abbasi
Binding of a molecule to protein contains four types of non-covalent interactions playing leading roles that include hydrophobic forces, electrostatic interactions, van der Waals, and hydrogen bonds [59]. The thermodynamic parameters can be used to specify the type of force between the complex and HSA. The laws of thermodynamics are applied to compute the data of ΔH0 and ΔS0. When ΔH0 > 0 and ΔS0 > 0, it means that the hydrophobic forces contributed to the binding. When ΔH0 < 0 and ΔS0 < 0, the hydrogen bonds and van der Waals forces are dominant and ΔH0 ≈ 0, ΔS0 > 0 is characteristic for electrostatic forces [60]. The van’t Hoff equation (eq. S6) is used to compute the ΔH0 and ΔS0.
Spectrophotometric and physicochemical studies on the interaction of a new platinum(IV) complex containing the drug pregabalin with calf thymus DNA
Published in Journal of Coordination Chemistry, 2020
Nahid Shahabadi, Sara Amiri, Hossein Zhaleh
Fluorescence is widely used in studying the mode of the interaction between a bio system and drug molecules. Various types of non-covalent interactions can play a role in the binding of a small molecule to a biomolecule including hydrogen bonds, van der Waals forces, electrostatic and hydrophobic interactions. According to the data of enthalpy changes (ΔH) and entropy changes (ΔS), the model of interaction can be concluded [42]: (a) ΔH > 0 and ΔS > 0, hydrophobic forces; (b) ΔH < 0 and ΔS < 0, van der Waals interactions and hydrogen bonds; and (c) ΔH < 0 and ΔS > 0, electrostatic interactions [43]. When there is little change of temperature, the enthalpy change (ΔH) can be seen as a constant, and then its value and that of entropy changes (ΔS) can be determined from the van’t Hoff equation (eq. (4)): where K is the binding constant at the corresponding temperature and R is gas constant. The values of ΔH and ΔS were obtained from the slope and intercept of the linear plot based on LnK versus 1/T. The values of ΔG were evaluated from the following equation (eq. (5)):