China
Africa
Explore chapters and articles related to this topic
Micronutrients
Published in Chuong Pham-Huy, Bruno Pham Huy, Food and Lifestyle in Health and Disease, 2022
Chuong Pham-Huy, Bruno Pham Huy
In general, an enzyme cannot function alone; it must be activated by one or many small molecules called coenzymes and cofactors. Some enzymes require several coenzymes and cofactors. Coenzymes and cofactors are small organic molecules or metal ions that are used by enzymes to help catalyze reactions (89–93). In other words, coenzymes are typically organic molecules that contain functionalities not found in proteins, while cofactors are catalytically essential molecules or ions that are covalently bound to enzymes (91). The term holoenzyme refers to an active enzyme complex: an enzyme combined with a coenzyme or a cofactor. An apoenzyme is an inactive enzyme: an enzyme without an activator (coenzyme or/and cofactor). The term prosthetic group is used to refer to minerals, activated vitamins, or other nonprotein compounds that are required for full enzyme activity (89–93). The prosthetic group remains bonded for the enzyme during the reaction. In some cases, the prosthetic group is covalently bound for its apoenzyme, while in other cases it is weakly bound to the active center by numerous weak interactions (93).
Distribution and Biological Functions of Pyruvate Carboxylase in Nature
Published in D. B. Keech, J. C. Wallace, Pyruvate Carboxylase, 2018
Biotin may be readily incorporated into the apoenzyme to form the active holoenzyme in permeabilized cells in situ353 and in cell-free extracts572,839 when supplied with MgATP. The enzymatic basis for this was reviewed briefly in Section II.B.4 and is considered to be essentially identical for all biotin-containing enzymes, except that in the case of the microbial pyruvate carboxylases studied to date, biotinylation of the apoenzyme is affected by its interaction with the allosteric effectors acetyl-CoA and aspartate. Thus, the omission of acetyl-CoA (usually present at 500 μM) from the pyruvate holocarboxylase synthesis incubation led to a 60% reduction in the formation of active enzyme, while inclusion of L-aspartate (1 m M), even in the presence of acetylCoA (500 μM), resulted in a 50% inhibition of the synthesis of the holoenzyme.839 Of the biotin analogs and precursors tested (viz., biocytin, biotin sulfone, biotin-D-sulf-oxide, biotin-L-sulfoxide, dethiobiotin, diaminobiotin, and 7,8-diaminopelargonic acid), only biocytin was able to produce active pyruvate carboxylase when incubated with MgATP and apoenzyme-rich permeabilized yeast cells.353 The slow rate achieved with biocytin suggested that this may have resulted from the hydrolysis of biocytin to biotin and lysine, since formation of biotinyl holoenzyme requires a free carboxyl group on the valeryl side chain of the biotin.468
Useful Principles for the Crystallization of Proteins
Published in Hartmut Michel, Crystallization of Membrane Proteins, 1991
The addition of ligands, substrates, and other small molecules has seen widespread use in protein crystallography, since it provides useful alternatives if the apoenzyme itself cannot be crystallized. Lactate dehydrogenase29, Staphylococcus nuclease,2 dihydrofolate reductase,48 hexokinase,90 and many others relied on effector addition, to some extent at least, in the growth of some particular crystal form.
An updated patent review of small-molecule ROS1 kinase inhibitors (2015–2021)
Published in Expert Opinion on Therapeutic Patents, 2022
Meng Liu, Jintian Dai, Mudan Wei, Qingshan Pan, Wufu Zhu
The present compound 17 in patent AU2015100840A4 had a similar binding mechanism to ROS1 as Crizotinib. The molecular docking result of the most potent compound 17 with apoenzyme (ROS1 without endogenous ligand, PDB code: 4UXL) by Autodock 4.0 software was shown in the Figure 12. Compound 17 exhibited a better binding affinity to ROS1 than Crizotinib, the pyridine groups of the both compounds formed a hydrogen bond with Met2029 in the hinge region and the phenyl group, anisole group of this compound have formed extra hydrophobic interaction with the hinge and G-loop, respectively. what’s more, residues Leu 2028, Met2029, Glu2030, Gly2032, and Asp2033 in the hinge region have contacted with compound 17, and the residues Leu1951, Leu1959 in the G-loop formed hydrophobic interaction with compound 17 at the same time. The MTT assay showed that compound 17 was a potent inhibitor of HCC78 cells with an IC50 of 1.62 ± 0.39 μM, which has emerged much lower cytotoxicity on normal lung epithelial cells with an IC50 of 6.08 μM±1.16 μM. Representative compound 18 in patent AU2015101598A4 has introduced a thiophene into the 1,2,3,4-tetrahydroquinoline nucleus and the IC50 valued of the compound 18 on HCC78 cells was 6.35 ± 1.44 μM with advantageously lower cytotoxicity on normal lung cells, indicating that the compound 18 proved to be highly selective toward cancerous cells [61,62].
Targeting citrullination in autoimmunity: insights learned from preclinical mouse models
Published in Expert Opinion on Therapeutic Targets, 2021
Ylke Bruggeman, Fernanda M.C. Sodré, Mijke Buitinga, Chantal Mathieu, Lut Overbergh, Maria J.L. Kracht
A better understanding of the biochemical process of protein citrullination and high-resolution X-ray crystal structures of the PAD isozymes led to the development of compounds with enhanced potency, isozyme-specificity and in vivo stability and efficacy [52]. This includes the discovery of inhibitors that preferentially bind the apoenzyme [53,54], as opposed to Cl-amidine and BB-Cl-amidine which require the conformational changes induced by calcium binding. Examples of potent isozyme-specific inhibitors are: D-o-F-amidine [55], a PAD1 inhibitor; AFM30a [34], a PAD2 inhibitor; compound 14b [56], a PAD3 inhibitor; and GSK199 [54], an apoenzyme PAD4 inhibitor. GSK199 has been proven to reduce citrullination and NET formation in neutrophils [54] and has already been evaluated for its therapeutic efficacy in a mouse model for RA [57]. Like PAD4, PAD2 is highly expressed in immune cell populations and implicated in regulation of the immune response. To our knowledge, PAD2-specific inhibition has not yet been evaluated as potential treatment for autoimmunity. AFM30a could be a suitable candidate for in vivo applications due to superior selectivity to PAD2 over PAD4 and promising cell-based efficacy [34]. However, AFM30a still retains inhibitory potency for PAD1. Of note, while some inhibitors are described as being isozyme-specific, the inactivation kinetics indicate inhibitory potencies for other isozymes as well, as apparent from details provided in Table 1. This is especially the case for inhibitors designed for PAD2.
Unveiling the interaction profile of rosmarinic acid and its bioactive substructures with serum albumin
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2020
Christina Papaemmanouil, Maria V. Chatziathanasiadou, Christos Chatzigiannis, Eleni Chontzopoulou, Thomas Mavromoustakos, Simona Golic Grdadolnik, Andreas G. Tzakos
Bovine serum albumin (BSA) homodimer crystal structure was downloaded from the Protein Data Bank (https://www.rcsb.org/). The downloaded structure of BSA (PDB ID: 4F5S) constitutes the crystal structure of the apoenzyme – protein. BSA complexes with various bioactive molecules were not used in the study as the ligands deviated structurally with those under study. The homodimer protein was prepared using Maestro’s Protein Preparation Wizard. During this preparation, missing loops and side chains were fixed using Prime algorithm. Water molecules beyond 5 Å from het groups were deleted, disulphide bonds among Cys residues were created and hydrogens were added to the crystal structure. Overlapping atoms were minimised and different alternate positions of side chains were committed to a single one. Chain B of each homodimer was deleted to accelerate docking process. PROPKA was used to identify the protonation states of amino acids at neutral pH and OPLS3 force field was applied in order to minimise hydrogen atoms of the protein.