24 articles for “Docking Interaction”

Research ArticleOpen accessPhrase in the titleHOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDIES OF EC1 DOMAIN OF VE-CADHERIN TO ELUCIDATE DOCKING INTERACTION WITH CADHERIN-DERIVED PEPTIDEVivitri Dewi Prasasty, Usman Sumo Friend Tambunan, Teruna Jaya SiahaanVE-cadherin is a protein in the cadherin family that is found at the adherens junctions of the microvessel endothelial cells of the Blood-Brain Barrier (BBB). It is recognized as the homotypic cell adhesion molecules and there is limited structural information on how VE-cadherins mediate cell-cell adhesion. It has been shown that the EC1 domain of cadherins is important for the … …OnLine Journal of Biological Sciences, Vol. 14, Issue 2 · 25 Jun 2014 · 7,530 accessesView PDF Cite

Research ArticleOpen accessEvery word in the titleThe Effect of Trilobatin on Bovine Serum Albumin: Interaction Mechanism and Molecular DockingYuhan Zhai, Yuqing Zhang, Yaping Li et al.Understanding the transport and distribution of small molecules in vivo is aided by studying their interactions with proteins. As a natural sweetener, trilobatin possesses several biological activities. However, uncertainty surrounds the trilobatin and Bovine Serum Albumin (BSA) interaction mechanism. In this study, the binding types, number of binding sites and binding constants of trilobatin interaction with BSA were studied by … …American Journal of Biochemistry and Biotechnology, Vol. 20, Issue 1 · 29 Mar 2024 · 4,843 accessesView PDF Cite

Research ArticleOpen accessIn the keywordsComputer Aid Screening for Potential Antimalarial Choroquinone Compounds as Covid 19 Utilizing Computational Calculations and Molecular Docking StudyAsmaa Aboelnaga, Asmaa M. Fahim, Taghreed H. EL-SayedClick reaction of 4,7-dichloroquinoline (1) with thiosemicarbazide (2) to afford the corresponding 2-(7-chloroquinolin-4-yl)thiosemicarbazide (3) utilized ultrasonic irradiation which can cyclized easily with ethylacetoacetate to give the 3-(7-chloroquinolin-4-ylamino)-tetrahydro-6-methyl-2-thioxopyrimidin-4(1H)-one (4) via nucleophilic substitution reaction. The synthesized compounds was examined in vitro antimalarial activity with IC50 = 11.92, 25.37 μg/mL against chloroquinone drug. Furthermore, the theoretical investigation of most active compounds CQT and … …OnLine Journal of Biological Sciences, Vol. 20, Issue 4 · 30 Nov 2020 · 6,568 accessesView PDF Cite

Research ArticleOpen accessIn the abstractUnveiling the Potential of Dombeya buettneri K.Schum As a Drug Agent: Molecular Docking of Compounds With Enzymes Linked to Diabetes and Neurodegenerative DiseaseEsther Emem Nwanna, Samuel Chima Ugbaja et al.This study investigated the mechanisms of Dombeya buettneri (snowball leafy) extracts on diabetes, hypertension, and neurodegenerative diseases. It compared extracts obtained using steep water (a by-product of corn wet milling) and aqueous water. The extracts were analyzed for total phenol, total flavonoid content, antioxidant activities such as FRAP, ABTS, NO, DPPH, iron-induced lipid peroxidation assay, degradation of deoxyribose (Fenton’s reaction), … …OnLine Journal of Biological Sciences, Vol. 25, Issue 4 · 1 Feb 2026 · 2,025 accessesView PDF Cite

Research ArticleOpen accessIn the abstractComputational Validation of Selected Compounds from the GC-MS Profile of Abies numidica Essential Oil and their Antibacterial EffectsAbdelouahab Dehimat, Boudjellal Fayssal, Salem Dounya et al.This work examined the chemical composition of the Algerian endemic tree Abies numidica (Pinaceae) and investigated the antibacterial potential of three major constituents of its essential oil-Santene, Linalyl acetate, and 2,6-Octadiene-2,6-dimethyl-as reported in previously published GC-MS data. Computational antibacterial screening was carried out by docking the selected compounds onto the bacterial proteins 5Z9N (Staphylococcus aureus) and 3AQC (Micrococcus luteus). Molecular … …Current Research in Bioinformatics, Vol. 10, Issue 1 · 24 Jan 2026 · 2,939 accessesView PDF Cite

Research ArticleOpen accessIn the abstractIn silico and in vitro Structural Analysis on the Interaction of Calmodulin and Calmodulin-Binding Motif of FKBP35 from Plasmodium knowlesiSazlinawatie Aladin, Cahyo Budiman et al.FK506-binding protein 35 (FKBP35) is a peptidyl-prolyl cis-trans isomerase found in Plasmodium knowlesi, a zoonotic malaria parasite responsible for concerning cases of malaria infection in East Malaysia. This protein contains a segment known as the calmodulin-binding motif (Pk-CBM), which is predicted to facilitate interaction with calmodulin from P. knowlesi (Pk-CaM). Although this interaction is considered promising for future antimalarial drug … …OnLine Journal of Biological Sciences, Vol. 25, Issue 2 · 10 Mar 2025 · 4,846 accessesView PDF Cite

Research ArticleOpen accessIn the abstractThe Effect of NaCl on the Stability of Ab3 Lipase from Sphingobacterium sp. that Co-Expressed with LEA K Using In silico ApproachIbrahim Muhammad et al.This study explores how sodium chloride (NaCl) influences the binding affinity and stability of the Ab3 lipase-LEA K complex when interacting with olive oil, using molecular docking techniques. The docking simulations, conducted with AutoDock Vina, reveal that the presence of NaCl significantly enhances the binding affinity of the enzyme-substrate complex, increasing it from-6.55 kcal/mol in the absence of salt to-7.81 … …American Journal of Biochemistry and Biotechnology, Vol. 21, Issue 1 · 9 Mar 2025 · 5,599 accessesView PDF Cite

Research ArticleOpen accessIn the abstractInvestigation of the Contribution of Late Embryogenesis Abundant (LEA) K Peptide in Enhancing the Expression of Lipase from Sphingobacterium sp.: In vitro and in Silico StudiesIbrahim Muhammad et al.Sphingobacterium sp. AB3 lipase is a psychrophilic enzyme with optimal lipolytic activity at pH 7 and 15°C. The cold-adapted properties of the lipase render it suitable for various low-temperature industrial applications such as biodiesel production, detergent formulation, and non-thermal food processing. Recent studies have shown that co-expression of LEA K peptide with AB3 lipase resulted in enhanced protein expression in … …American Journal of Biochemistry and Biotechnology, Vol. 20, Issue 4 · 21 Nov 2024 · 4,569 accessesView PDF Cite

Research ArticleOpen accessIn the abstractMechanism Analysis of Artemisinin and Artesunate as Lung Cancer Therapy Agents Through in Silico MethodDidik Harmoko, Vivitri Dewi Prasasty, Adi YulandiSeveral in vitro studies have focused on the ability of artemisinin and its derivatives to suppress lung cancer cells, but there are still many biological processes and mechanisms, such as the interactions between the active compounds (ligands) and receptors that are not well understood and require further research. Drug targeting for lung cancer will be more precise and the inhibition … …OnLine Journal of Biological Sciences, Vol. 24, Issue 3 · 15 Feb 2024 · 6,144 accessesView PDF Cite

Research ArticleOpen accessIn the abstractEnhancement of Geobacillus thermodenitrificans Lipase Activity and Binding Affinity by Acetone Treatment: Kinetic and in silico InvestigationsAmmar Khazaal Kadhim Almansoori, Alyaa Abdulhussein Alsaedi et al.Lipase Geobacillus thermodenitrificans (LipGt) is a thermostable enzyme that has an optimal activity temperature of 65°C. It can tolerate various organic solvents and has an improved activity, especially in the presence of acetone. In this study, in-vitro and in-silico studies were carried out to investigate the effect of acetone in enhancing the kinetic and binding affinity of LipGt. The LipGt … …American Journal of Biochemistry and Biotechnology, Vol. 20, Issue 4 · 10 Oct 2024 · 4,817 accessesView PDF Cite