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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
Modern drug design requires the discovery and classification of protein ligand binding sites as well as their interfaces with binding associates. SMAP, a software tool, was created with these objectives in mind. SMAP surpasses the majority of existing ligand binding site comparison tools; however, it lacks the scalability and availability required for large database searches.
Magnetic Nanosensors
Published in Vinod Kumar Khanna, Nanosensors, 2021
Research on nanoparticles of metals and semiconductors has been extensively pursued worldwide because of the unique electronic and optical properties of nanoparticles. When coupled to affinity ligands, such nanoparticles function as sensitive biological nanosensors. A ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The interaction of ligands with their binding sites is characterized in terms of a binding affinity. In general, high-affinity ligand binding results from greater intermolecular force between the ligand and its receptor, whereas low-affinity ligand binding involves smaller intermolecular force between the ligand and its receptor.
Ligand Binding to Macromolecules
Published in Jean-Louis Burgot, Thermodynamics in Bioenergetics, 2019
The binding site of a protein is the place where the ligand binds. The binding site is complementary to the ligand in size, charge, shape and hydrophobic and hydrophilic character. Furthermore, the interaction is specific. A protein may often have several sites.
Urease inhibition and anti-leishmanial properties of Zn(II) complexes of thiophenyl and furyl-derived C 2-symmetric ligands
Published in Journal of Coordination Chemistry, 2022
Saira Nayab, Momin Khan, Yerim Cho, Hyosun Lee
Many functional proteins and enzymes contain active sites within their structures that function as binding sites for ligand molecules. These binding sites can be exploited to switch the functions of such enzymes on and off. In this context, virtual docking of enzyme active sites is an important process facilitating an understanding of the mechanism of enzyme action as well as in rational drug design. In this context, 1-4 were docked into the active pocket of JB urease; stable enzyme complexes were predicted based on the lowest energy, lowest root-mean-square deviation (RMSD) values, and highest scoring. The active site residues of the JB urease are HIS137, HIS139, ALA170, HIS222, HIS249, HIS275, GLY280, and ASP363, along with two Ni+3 ions.
HPLC-MS/MS chemical characterization and biological properties of Origanum onites extracts: a recent insight
Published in International Journal of Environmental Health Research, 2019
Mohamad Fawzi Mahomoodally, Gokhan Zengin, Mustafa Onur Aladag, Haluk Ozparlak, Alina Diuzheva, József Jekő, Zoltán Cziáky, Muhammad Zakariyyah Aumeeruddy
The use of plant-based enzyme inhibitors is encouraged nowadays because there is concern about the side effects associated with synthetic pharmaceutical agents. Enzyme inhibition involves an enzyme-substrate reaction influenced by covalent or non-covalent interactions with enzyme active site. The structure and chemistry of natural ligand binding sites on enzymes makes it suitable for interactions with small, drug-like molecules, thereby modulating their activity (Copeland et al. 2007).
Microwave-assisted Multi-component Reaction for the Green Synthesis of Novel 4-(5-hydroxybenzo[a]phenazin-6-yl)-5-phenyl-1, 3-dihydro-2H-imidazol-2-one Using H3PW12O40@nano-TiO2 as Recyclable Catalyst
Published in Green Chemistry Letters and Reviews, 2022
Milad Taheri, Zanko Hassan Jawhar
In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate (binding site) and residues that catalyze a reaction of that substrate (catalytic site). Although the active site occupies only ∼10–20% of the volume of an enzyme, is the most important part as it directly catalyzes the chemical reaction (22).