Correction to Competitive Inhibition Mechanism of Acetylcholinesterase without Catalytic Active Site Interaction: Study on Functionalized C60 Nanoparticles via in Vitro and in Silico Assays

Background: Melanogenesis is a process of melanin synthesis, which is a primary response for the pigmentation of human skin. Tyrosinase is a key enzyme, which catalyzes a ratelimiting step of the melanin formation. Natural products have shown potent inhibitors, but some of these possess toxicity. Numerous synthetic inhibitors have been developed in recent years may lead to the potent anti– tyrosinase agents. Objective: A number of 4-hydroxy-N'-methylenebenzohydrazide analogues with related structure to chalcone and tyrosine were constructed with various substituents at the benzyl ring of the molecule and evaluate as a tyrosinase inhibitor. In addition, computational analysis and metal chelating potential have been evaluated. Methods: Design and synthesized compounds were evaluated for activity against mushroom tyrosinase. The metal chelating capacity of the potent compound was examined using the mole ratio method. Molecular docking of the synthesized compounds was carried out into the tyrosine active site. Results: Novel 4-hydroxy-N'-methylenebenzohydrazide derivatives were synthesized. The two compounds 4c and 4g showed an IC50 near the positive control, led to a drastic inhibition of tyrosinase. Confirming in vitro results were performed via the molecular docking analysis demonstrating hydrogen bound interactions of potent compounds with histatidine-Cu+2 residues with in the active site. Kinetic study of compound 4g showed competitive inhibition towards tyrosinase. Metal chelating assay indicates the mole fraction of 1:2 stoichiometry of the 4g-Cu2+ complex. Conclusion: The findings in the present study demonstrate that 4-Hydroxy-N'- methylenebenzohydrazide scaffold could be regarded as a bioactive core inhibitor of tyrosinase and can be used as an inspiration for further studies in this area.

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In Silico Appraisal, Synthesis, Antibacterial Screening and DNA Cleavage for 1,2,5-thiadiazole Derivative

Current Computer - Aided Drug Design ◽

10.2174/1573409915666190206142756 ◽

2019 ◽

Vol 15 (5) ◽

pp. 445-455 ◽

Cited By ~ 6

Author(s):

Suraj N. Mali ◽

Sudhir Sawant ◽

Hemchandra K. Chaudhari ◽

Mustapha C. Mandewale

Keyword(s):

Molecular Docking ◽

Dna Cleavage ◽

In Silico ◽

Oral Absorption ◽

Inhibition Mechanism ◽

Hydrogen Binding ◽

Docking Score ◽

Antibacterial Screening ◽

Mycobacteria Tuberculosis

Background: : Thiadiazole not only acts as “hydrogen binding domain” and “two-electron donor system” but also as constrained pharmacophore. Methods:: The maleate salt of 2-((2-hydroxy-3-((4-morpholino-1, 2,5-thiadiazol-3-yl) oxy) propyl) amino)- 2-methylpropan-1-ol (TML-Hydroxy)(4) has been synthesized. This methodology involves preparation of 4-morpholino-1, 2,5-thiadiazol-3-ol by hydroxylation of 4-(4-chloro-1, 2,5-thiadiazol-3-yl) morpholine followed by condensation with 2-(chloromethyl) oxirane to afford 4-(4-(oxiran-2-ylmethoxy)-1,2,5-thiadiazol- 3-yl) morpholine. Oxirane ring of this compound was opened by treating with 2-amino-2-methyl propan-1- ol to afford the target compound TML-Hydroxy. Structures of the synthesized compounds have been elucidated by NMR, MASS, FTIR spectroscopy. Results: : The DSC study clearly showed that the compound 4-maleate salt is crystalline in nature. In vitro antibacterial inhibition and little potential for DNA cleavage of the compound 4 were explored. We extended our study to explore the inhibition mechanism by conducting molecular docking, ADMET and molecular dynamics analysis by using Schrödinger. The molecular docking for compound 4 showed better interactions with target 3IVX with docking score of -8.508 kcal/mol with respect to standard ciprofloxacin (docking score= -3.879 kcal/mol). TML-Hydroxy was obtained in silico as non-carcinogenic and non-AMES toxic with good percent human oral absorption profile (69.639%). TML-Hydroxy showed the moderate inhibition against Mycobacteria tuberculosis with MIC 25.00 μg/mL as well as moderate inhibition against S. aureus, Bacillus sps, K. Pneumoniae and E. coli species. Conclusion: : In view of the importance of the 1,2,5-thiadiazole moiety involved, this study would pave the way for future development of more effective analogs for applications in medicinal field.

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Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus : In silico and in vitro perspective

Journal of Cellular Biochemistry ◽

10.1002/jcb.27261 ◽

2018 ◽

Vol 119 (11) ◽

pp. 9444-9461 ◽

Cited By ~ 4

Author(s):

Rishikesh Satish Parulekar ◽

Kailas Dashrath Sonawane

Keyword(s):

Antibiotic Resistance ◽

Bacillus Cereus ◽

In Silico ◽

Inhibition Mechanism ◽

Aminoglycoside Phosphotransferase

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Phenoxyethyl Piperidine/Morpholine Derivatives as PAS and CAS Inhibitors of Cholinesterases: Insights for Future Drug Design

Scientific Reports ◽

10.1038/s41598-019-56463-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Yaghoub Pourshojaei ◽

Ardavan Abiri ◽

Khalil Eskandari ◽

Zahra Haghighijoo ◽

Najmeh Edraki ◽

...

Keyword(s):

Conformational Changes ◽

Active Site ◽

Inhibitory Activity ◽

Reference Drug ◽

Catalytic Active Site ◽

Electric Eel ◽

Interesting Candidate ◽

Future Drug ◽

Morpholine Derivatives

AbstractAcetylcholinesterase (AChE) catalyzes the conversion of Aβ peptide to its aggregated form and the peripheral anionic site (PAS) of AChE is mainly involved in this phenomenon. Also catalytic active site (CAS) of donepezil stimulates the break-down of acetylcholine (ACh) and depletion of ACh in cholinergic synapses are well established in brains of patients with AD. In this study, a set of compounds bearing phenoxyethyl amines were synthesized and their inhibitory activity toward electric eel AChE (eeAChE) and equine butyrylcholinesterase (eqBuChE) were evaluated. Molecular dynamics (MD) was employed to record the binding interactions of best compounds against human cholinesterases (hAChE and hBuChE) as well as donepezil as reference drug. In vitro results revealed that compound 5c is capable of inhibiting eeAChE activity at IC50 of 0.50 µM while no inhibitory activity was found for eqBuChE for up to 100 µM concentrations. Compound 5c, also due to its facile synthesis, small structure and high selectivity for eeAChE would be very interesting candidate in forthcoming studies. The main interacting parts of compound 5c and compound 7c (most potent eeAChE and eqBuChE inhibitors respectively) with receptors which confer selectivity for AChE and BuChE inhibition were identified, discussed, and compared with donepezil’s interactions. Also during MD simulation it was discovered for the first time that binding of substrates like donepezil to dual CAS and PAS or solely CAS region might have a suppressive impact on 4-α-helical bundles near the tryptophan amphiphilic tetramerization (WAT) domain of AChE and residues which are far away from AChE active site. The results proposed that residues involved in donepezil interactions (Trp86 and Phe295) which are located in CAS and mid-gorge are the mediator of conformational changes in whole protein structure.

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Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode

Biochemical Journal ◽

10.1042/bcj20190288 ◽

2019 ◽

Vol 476 (12) ◽

pp. 1843-1856 ◽

Cited By ~ 1

Author(s):

Cyril Hamiaux ◽

Lesley Larsen ◽

Hui Wen Lee ◽

Zhiwei Luo ◽

Prachi Sharma ◽

...

Keyword(s):

In Silico ◽

Binding Mode ◽

Crystal Structure Analysis ◽

Tolfenamic Acid ◽

In Vitro Assays ◽

Inhibition Mechanism ◽

In Planta ◽

Competitive Antagonist ◽

In Silico Docking

Abstract Strigolactones (SLs) are multifunctional plant hormones regulating essential physiological processes affecting growth and development. In vascular plants, SLs are recognized by α/β hydrolase-fold proteins from the D14/DAD2 (Dwarf14/Decreased Apical Dominance 2) family in the initial step of the signaling pathway. We have previously discovered that N-phenylanthranilic acid derivatives (e.g. tolfenamic acid) are potent antagonists of SL receptors, prompting us to design quinazolinone and quinazolinedione derivatives (QADs and QADDs, respectively) as second-generation antagonists. Initial in silico docking studies suggested that these compounds would bind to DAD2, the petunia SL receptor, with higher affinity than the first-generation compounds. However, only one of the QADs/QADDs tested in in vitro assays acted as a competitive antagonist of SL receptors, with reduced affinity and potency compared with its N-phenylanthranilic acid ‘parent’. X-ray crystal structure analysis revealed that the binding mode of the active QADD inside DAD2's cavity was not that predicted in silico, highlighting a novel inhibition mechanism for SL receptors. Despite a ∼10-fold difference in potency in vitro, the QADD and tolfenamic acid had comparable activity in planta, suggesting that the QADD compensates for lower potency with increased bioavailability. Altogether, our results establish this QADD as a novel lead compound towards the development of potent and bioavailable antagonists of SL receptors.

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ATIVIDADE INIBITÓRIA DE PESTICIDAS PIRETROIDES SOBRE A GLUTATIONA S-TRANSFERASE

Química Nova ◽

10.21577/0100-4042.20170804 ◽

2021 ◽

Author(s):

Eliane Ribeiro ◽

Mihaela Badea ◽

Danilo Ribeiro ◽

Andressa Costa ◽

Djanira dos Santos ◽

...

Keyword(s):

Surface Waters ◽

In Silico ◽

Competitive Inhibition ◽

Environmental Contaminants ◽

The Other ◽

Inhibition Mechanism ◽

Glutathione S Transferase ◽

Pyrethroid Pesticides ◽

Rivers And Lakes ◽

Ic50 Values

INHIBITORY ACTIVITY OF PYRETHROID PESTICIDES ON GLUTATHIONE S-TRANSFERASE. Glutathione S-transferase (GST) is one of the enzymes used to evaluate the effects caused by environmental contaminants. The aim of this work was to study the effects of four pyrethroid compounds (allethrin, cypermethrin, deltamethrin and fenpropathrin) on the catalytic activity of GST and to estimate the potential for environmental contamination in silico of these insecticides. Spectrophotometric analyses showed that the activity of the GST enzyme was inhibited by the four pesticides, with the values for the inhibition constant (Ki) varying from 0.12 to 20 µmol L-1, with the following order of inhibition from the highest to the lowest Ki value: deltamethrin > cypermethrin > allethrin > fenpropathrin. They presented a competitive and non-competitive inhibition mechanism depending on the compound. The IC50 values (concentration that inhibits 50% of the enzyme activity) showed the insecticide deltamethrin with greater inhibitory capacity, since it reduced the activity of the GST enzyme by half, even though it was in a lower concentration in relation to the other analyzed compounds. The in silico evaluation indicated the possibility of most of the insecticides contaminating the surface waters (rivers and lakes) adhered to the suspended sediment, but did not show any potential for contamination of groundwater through leaching.

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Crambescin C1 Acts as A Possible Substrate of iNOS and eNOS Increasing Nitric Oxide Production and Inducing In Vivo Hypotensive Effect

Frontiers in Pharmacology ◽

10.3389/fphar.2021.694639 ◽

2021 ◽

Vol 12 ◽

Author(s):

Juan A. Rubiolo ◽

Emilio Lence ◽

Concepción González-Bello ◽

María Roel ◽

José Gil-Longo ◽

...

Keyword(s):

Nitric Oxide ◽

Active Site ◽

In Silico ◽

Hypotensive Effect ◽

Docking Studies ◽

No Production ◽

Guanidine Alkaloids ◽

Endogenous Substrate

Crambescins are guanidine alkaloids from the sponge Crambe crambe. Crambescin C1 (CC) induces metallothionein genes and nitric oxide (NO) is one of the triggers. We studied and compared the in vitro, in vivo, and in silico effects of some crambescine A and C analogs. HepG2 gene expression was analyzed using microarrays. Vasodilation was studied in rat aortic rings. In vivo hypotensive effect was directly measured in anesthetized rats. The targets of crambescines were studied in silico. CC and homo-crambescine C1 (HCC), but not crambescine A1 (CA), induced metallothioneins transcripts. CC increased NO production in HepG2 cells. In isolated rat aortic rings, CC and HCC induced an endothelium-dependent relaxation related to eNOS activation and an endothelium-independent relaxation related to iNOS activation, hence both compounds increase NO and reduce vascular tone. In silico analysis also points to eNOS and iNOS as targets of Crambescin C1 and source of NO increment. CC effect is mediated through crambescin binding to the active site of eNOS and iNOS. CC docking studies in iNOS and eNOS active site revealed hydrogen bonding of the hydroxylated chain with residues Glu377 and Glu361, involved in the substrate recognition, and explains its higher binding affinity than CA. The later interaction and the extra polar contacts with its pyrimidine moiety, absent in the endogenous substrate, explain its role as exogenous substrate of NOSs and NO production. Our results suggest that CC serve as a basis to develop new useful drugs when bioavailability of NO is perturbed.

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Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E

Nucleic Acids Research ◽

10.1093/nar/gkz1152 ◽

2019 ◽

Vol 48 (2) ◽

pp. 847-861 ◽

Cited By ~ 2

Author(s):

Nida Ali ◽

Jayaraman Gowrishankar

Keyword(s):

Escherichia Coli ◽

Active Site ◽

Rna Binding ◽

Initial Step ◽

Dominant Negative ◽

Rnase E ◽

Wild Type ◽

Catalytic Active Site

Abstract RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5′-sensor pocket that renders enzyme activity maximal on 5′-monophosphorylated RNAs. The protein's non-catalytic C-terminal half (CTH) harbours RNA-binding motifs and serves as scaffold for a multiprotein degradosome complex, but is dispensable for viability. Here, we provide evidence that a full-length hetero-tetramer, composed of a mixture of wild-type and (recessive lethal) active-site mutant subunits, exhibits identical activity in vivo as the wild-type homo-tetramer itself (‘recessive resurrection’). When all of the cognate polypeptides lacked the CTH, the active-site mutant subunits were dominant negative. A pair of C-terminally truncated polypeptides, which were individually inactive because of additional mutations in their active site and 5′-sensor pocket respectively, exhibited catalytic function in combination, both in vivo and in vitro (i.e. intragenic or allelic complementation). Our results indicate that adjacent subunits within an oligomer are separately responsible for 5′-sensing and cleavage, and that RNA binding facilitates oligomerization. We propose also that the CTH mediates a rate-determining initial step for enzyme function, which is likely the binding and channelling of substrate for NTH’s endonucleolytic action.

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Antibiotics Used in Patients after Surgery and Effects of Human Serum Paraoxonase-I (PON1) Enzyme Activity

Protein and Peptide Letters ◽

10.2174/0929866526666190124144622 ◽

2019 ◽

Vol 26 (3) ◽

pp. 215-220 ◽

Cited By ~ 1

Author(s):

Aycan Yılmaz ◽

Esra Dilek

Keyword(s):

Enzyme Activity ◽

Human Serum ◽

Active Site ◽

Active Agent ◽

Cefuroxime Axetil ◽

Inhibition Mechanism ◽

Paraoxonase Activity ◽

Activity Measurements ◽

Active Substances

Background: Paraoxonase (PON; arilesterase, [EC 3.1.8.1]) is an enzyme from the group arilesterases (ARE). This enzyme is capable of hydrolyzing paraoxone which is the active metabolite of parathion, an organic phosphorus insecticide. PON activity was found to be low in individuals prone to development of atherosclerosis such as diabetes, familial hypercholesterolemia and kidney disorders. It was noted that PON enzyme activity decreases in relation to age increase in adults. PON enzyme activity is approximately half of that in newborns and premature babies. Approximately one year after birth, it reaches the adult level. It can be said that PON1 has significant role on living organisms. For this reason, many studies on interactions of PON-drugs are needed. </P><P> Objective: In this article, our aim is to investigate in vitro effects of four pharmaceutically active agents (fosfomycin, cefuroxime axetil, cefaclor monohydrate, and cefixime) which are often used in patients after surgery on human serum paraoxanase-I (PON1) enzyme activity. Methods: In this article, we purify paraoxonase-I enzyme from human serum by using ammonium sulfate precipitation (in the range of 60-80%), ion exchange and gel filtration chromatography. We use electrophoresis to check the purity of the enzyme. We investigate the paraoxonase activity of the enzyme at 412 nm the inhibition effects of the active substances. Paraoxone is used as the substrate. Activity measurements arw made at different inhibitor concentrations related to inhibitor studies and % Activity- [I] graphs are drawn for drug active substances. Lineweaver-Burk graphics are used to determine the Ki constants. Finally, to determine the types of inhibition we interpret these graphs. Results: The active agents used after surgery decreased the PON1 enzyme activity. They showed different inhibition mechanism. The inhibition mechanism of fosfomycin and cefaclor monohydrate was noncompetitive, cefixime was uncompetitive and cefuroxime axetil was a competitive inhibitor. The IC50 values for fosfomycin, cefuroxime axetil, cefaclor monohydrate, and cefixime were calculated to be 31.5 mM, 1.03 mM, 4.18 mM and 0.781 mM, respectively, and the Ki constants were determined to be 27.98 ± 12.25 mM, 2.20 ± 0.22 mM, 4.81 ± 2.25 mM and 1.12 ± 0.32 mM, respectively. The IC50 and Ki values showed that cefixime active agent has the maximum inhibition. Conclusion: In this study, we have detected that cefuroxime axetil inhibited competitively in vitro paraoxonase activity of this enzyme. According to this information, we thought that cefuroxime axetil linked to the active site of the enzyme. Fosfomycin and cefaclor monohydrate can be attached with amino acids out of the active site of the enzyme because they inhibit enzyme noncompetitively. Cefixime can be attached only to the enzyme-substrate complex because it inhibits enzyme uncompetitively.

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