Computational Docking Studies Research Articles

Computational design, docking, and molecular dynamics simulation study of RNA helicase inhibitors of dengue virus.

RNA viruses are complex pathogens in terms of their genetic makeup, mutation frequency, and transmission modes. They contain the RNA helicase enzyme, which plays a crucial role in the viral genome replication process. This work aims to develop and screen a potential molecule that could function as a dengue virus (DENV) RNA helicase inhibitor. The present study was performed by taking 26 potential derivatives of gedunin phytochemicals from the PubChem database as ligands. The binding study of the compounds were analyzed by in silico docking method considering DENV RNA helicase enzyme as the receptor. After a thorough analysis of the docking scores, toxicity, and physicochemical properties, compound tetrahydrogedunin was obtained as the best. Based on tetrahydrogedunin molecular structure, 100 drug-like molecules were designed using the Data Warrior tool. After the screening process for drug-likeness and ADMET properties, the derivative number 42 was considered as the promising. Further comparative docking of derivative 42 and a standard inhibitor molecule ST-610 with DENV RNA helicase enzyme showed binding affinity as -10.0 kcal/mol and -9.6 kcal/mol, respectively. The favorable interaction between DENV RNA helicase and derivative 42 was further validated by 50 nanoseconds molecular dynamics simulation and MM-GBSA analysis. Since the antiviral activity of derivative 42 has not been reported till date, the compound was predicted as a novel therapeutic molecule that can act against the dengue virus (DENV) RNA helicase enzyme.

“Synergistic Innovation: Crafting Indazole Derivatives for Advanced Anticancer, Antioxidant, and Antimicrobial Efficacy through Integrative Design and Holistic Evaluation”

AbstractThis study presents the synthesis and characterization of a newer series of N‐(1‐(2‐(phenylamino) pyrimidin‐4‐yl)‐1H‐indazol‐5‐yl)benzenesulfonamide (6 a–6 n) and N‐(6‐ethoxy‐1‐(2‐(phenylamino) pyrimidin‐4‐yl)‐1H‐indazol‐5‐yl)benzenesulfonamide (7 a–7 c) derivatives through the reaction of N‐(1‐(2‐chloropyrimidin‐4‐yl)‐1H‐indazol‐5‐yl) benzenesulfonamide (4 a–i) and N‐(1‐(2‐chloropyrimidin‐4‐yl)‐6‐ethoxy‐1H‐indazol‐5‐yl) benzenesulfonamide (5 a–i) with various aniline derivatives in isopropanol. The compounds were thoroughly evaluated for their biological activities, encompassing antifungal, antibacterial, and anticancer assays, as well as antioxidant potential in DPPH and ABTS assays. Compound 7 b (IC50: 0.0125 MIC), 6 e (IC50: 0.0128 MIC), and 6 i (IC50: 0.0128 MIC) demonstrated exceptional antibacterial efficacy, while 6 d (IC50: 0.0124 MIC), 6 f (IC50: 0.0125 MIC) and 7 c (IC50: 0.0118 MIC), exhibited notable antifungal activity. Compounds 6 c (IC50: 13.31±0.32 μM, A459) & (IC50: 22.36±1.76 μM, MCF7) displayed significant anticancer activity comparable to established drugs. Moreover, 6 b (IC50: 11.22±0.16 μM, A459) & (IC50: 18.21±1.32 μM, MCF7) and 6 d (IC50: 11.23±0.17 μM, A459) & (IC50: 18.31±1.41 μM, MCF7) showed remarkable anticancer potency. Notably, compound N‐(1‐(2‐(methyl(phenyl)amino)pyrimidin‐4‐yl)‐1H‐indazol‐5‐yl)‐4‐nitrobenzenesulfonamide (IC50:0.1090 μmol/mL for DPPH and IC50: 0.1286 μmol/mL for ABTS) exhibited the most significant antioxidant activity. Computational docking studies revealed robust binding interactions with target enzymes (PDB ID: 4JT3 for anticancer, PDB ID: 1EA1 for antifungal, PDB ID: 1KZN for antibacterial, PDB ID: 3SRG for antioxidant), supported by molecular dynamics simulations indicating consistent stability of the most potent compound within the binding sites of the target proteins. These findings underscore the therapeutic potential of these derivatives, warranting further investigation for potential clinical applications.

Design, Synthesis and Molecular Modeling Study of Radiotracers Based on Tacrine and Its Derivatives for Study on Alzheimer’s Disease and Its Early Diagnosis

From 1993 to 2013, tacrine was an approved drug for Alzheimer’s disease. Due to its strong inhibitory properties towards cholinesterase, tacrine causes an increase in the level of the neurotransmitter acetylcholine in the cholinergic system of the central nervous system. This work presents a review of articles in which tacrine or its derivatives labeled with the radionuclides 3H, 11C, 14C, 123I, 99mTc and 68Ga were used as vectors in radiotracers dedicated to the diagnosis of Alzheimer’s disease. The possibility of clinical applications of the obtained radiopreparations was assessed by analyzing their physicochemical properties, ability to cross the blood–brain barrier and the level of uptake in the brain. Based on these data, it was shown that radiopreparations based on the tacrine molecule or its very close analogues retain the ability to cross the blood–brain barrier, while radiopreparations containing a more modified tacrine molecule (connected via a linker to a radionuclide chelator) lose this ability. This is probably the result of the addition of a chelator, which significantly increases the size of the radiopreparation and reduces its lipophilicity. Computer docking studies of tacrine derivatives and/or radiopreparations showed how these compounds bind to the active sites of acetyl- and butyrylcholinesterase.

A potential link between aromatics-induced oviposition repellency behaviors and specific odorant receptor of Aedes albopictus.

The Asian tiger mosquito, Aedes albopictus, is a competent vector for the spread of several viral arboviruses including dengue, chikungunya, and Zika. Several vital mosquito behaviors linked to survival and reproduction are primarily dependent on a sophisticated olfactory system for semiochemical perception. However, a limited number of studies has hampered our understanding of the relationship between the A. albopictus acute olfactory system and the complex chemical world. Here, we performed a qRT-PCR assay on antennae from A. albopictus of differing sex, age and physiological states, and found that AalbOr10 was enriched in blood-fed female mosquitoes. We then undertook single sensillum recording to de-orphan AalbOr10 using a panel of physiologically and behaviorally relevant odorants in a Drosophila 'empty neuron' system. The results indicated that AalbOr10 was activated by seven aromatic compounds, all of which hampered egg-laying in blood-fed mosquitoes. Furthermore, using a post-RNA interference oviposition assay, we found that reducing the transcript level of AalbOr10 affected repellent activity mediated by 2-ethylphenol at low concentrations (10-4 vol/vol). Computational modeling and molecular docking studies suggested that hydrogen bonds to Y68 and Y150 mediated the interaction of 2-ethylphenol with AalbOr10. We reveal a potential link between aromatics-induced oviposition repellency behaviors and a specific odorant receptor in A. albopictus. Our findings provide a foundation for identifying active semiochemicals for the monitoring or controlling of mosquito populations. © 2024 Society of Chemical Industry.

Molecular interactions by thermodynamic and computational molecular docking simulations of selected strawberry esters and pea protein isolate in an aqueous model system

The objective of this study was to determine the interactions between selected strawberry esters and pea protein isolate (PPI) in a protein-containing aqueous model system, utilizing modified ultrafiltration and equilibrium dialysis techniques. Strawberry esters, including ethyl butanoate, ethyl isopentanoate, ethyl hexanoate, and methyl anthranilate, demonstrated different binding parameters to the PPI. Overall flavor binding affinities (nK) of all esters decreased as the temperature increased from 5 °C to 25 °C. Among these compounds, ethyl hexanoate exhibited the highest affinity to PPI at 25 °C. Thermodynamic parameters revealed that all ester-PPI interactions were spontaneous and enthalpy-driven, primarily involving van der Waals forces or hydrogen bonding. In addition, computational molecular docking studies also identified alkyl hydrophobic interactions in ester-PPI complexes. These findings illustrated that understanding the interactions between esters and PPIs can assist in determining the optimal proportions of compounds for flavorings in high-protein beverages from pea protein.

Molecular and Structural Basis for Cγ-C Bond Formation by PLP-Dependent Enzyme Fub7.

Pyridoxal 5'-phosphate (PLP)-dependent enzymes that catalyze γ-replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP-dependent enzymes, CndF and Fub7, has unveiled unique C-C bond forming capabilities, enabling the biocatalytic synthesis of alkyl- substituted pipecolic acids from O-acetyl-L-homoserine and β-keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone-derived enolates as carbon nucleophiles, revealing Fub7's capacity for substrate-dependent regioselective α-alkylation of unsymmetrical ketones. Through an integrated approach combining X-ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.

Molecular and Structural Basis for Cγ−C Bond Formation by PLP‐Dependent Enzyme Fub7

AbstractPyridoxal 5’‐phosphate (PLP)‐dependent enzymes that catalyze γ‐replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP‐dependent enzymes, CndF and Fub7, has unveiled unique C−C bond forming capabilities, enabling the biocatalytic synthesis of alkyl‐ substituted pipecolic acids from O‐acetyl‐L‐homoserine and β‐keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone‐derived enolates as carbon nucleophiles, revealing Fub7’s capacity for substrate‐dependent regioselective α‐alkylation of unsymmetrical ketones. Through an integrated approach combining X‐ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.

CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism.

CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.

CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism

CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 – 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl–-permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl–-permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a “ball-and-chain” gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl–-permeation pathway.

1,3-Disubstituted-1,2,4-triazin-6-ones with potent activity against androgen receptor-dependent prostate cancer cells

Synthesis and biological evaluation of a small, focused library of 1,3-disubstituted-1,2,4-triazin-6-ones for in vitro inhibitory activity against androgen-receptor-dependent (22Rv1) and androgen-receptor independent (PC3) castration-resistant prostate cancer (CRPC) cells led to highly active compounds with in vitro IC50 values against 22Rv1 cells of <200 nM, and with apparent selectivity for this cell type over PC3 cells. From metabolic/PK evaluations of these compounds, a 3–benzyl-1–(2,4-dichlorobenzyl) derivative had superior properties and showed considerably stronger activity, by nearly an order of magnitude, against AR–dependent LNCaP and C4–2B cells compared to AR–independent DU145 cells. This lead compound decreased AR expression in a dose and time dependent manner and displayed promising therapeutic effects in a 22Rv1 CRPC xenograft mouse model. Computational target prediction and subsequent docking studies suggested three potential known prostate cancer targets: p38a MAPK, TGF-β1, and HGFR/c–Met, with the latter case of c–Met appearing stronger, owing to close structural similarity of the lead compound to known pyridazin-3-one derivatives with potent c-Met inhibitory activity. RNA-seq analysis showed dramatic reduction of AR signalling pathway and/or target genes by the lead compound, subsequently confirmed by quantitative PCR analysis. The lead compound was highly inhibitory against HGF, the c–Met ligand, which fitted well with the computational target prediction and docking studies. These results suggest that this compound could be a promising starting point for the development of an effective therapy for the treatment of CRPC.

Comparative investigation of derivatives of (E)-N-((E)-3-phenylallylidene)aniline: Synthesis, structural characterization, biological evaluation, density functional theory analysis, and in silico molecular docking

Bacterial resistance to antibiotics poses a significant global challenge for the public sector. Globally, researchers are actively investigating solutions to tackle the issue of bacterial resistance to antibiotics, with Schiff bases standing out as promising contenders in the fight against antimicrobial resistance. This study focused on synthesizing a series of Schiff bases (CA1-CA10) by reacting cinnamaldehyde with various aniline derivatives. Various analytical techniques, such as NMR, FTIR, UV–Vis, elemental analysis, and mass spectrometry, were employed to elucidate the structures of the synthesized compounds. Furthermore, crystal structure of CA8 was obtained using single crystal X-ray spectroscopy. The compounds were subjected to in vitro testing to assess their antibacterial and antifungal properties against eleven bacterial strains and four fungal strains. The results revealed diverse activity levels against the pathogens at varying concentrations, with notable potency observed in compounds CA3, CA4, CA9, and CA10, as indicated by their minimum inhibitory concentrations (MIC) values. The observed activity of the compounds seemed to be influenced by the specific substituents attached to their molecular structure. By conducting computational and molecular docking studies, the electronic properties of the compounds were investigated, further substantiating their potential as effective antimicrobial agents.

Characterization of Novel Trypanosoma cruzi-Specific Antigen with Potential Use in the Diagnosis of Chagas Disease.

Chagas disease is caused by the parasite Trypanosoma cruzi. In humans, it evolves into a chronic disease, eventually resulting in cardiac, digestive, and/or neurological disorders. In the present study, we characterized a novel T. cruzi antigen named Tc323 (TcCLB.504087.20), recognized by a single-chain monoclonal antibody (scFv 6B6) isolated from the B cells of patients with cardiomyopathy related to chronic Chagas disease. Tc323, a ~323 kDa protein, is an uncharacterized protein showing putative quinoprotein alcohol dehydrogenase-like domains. A computational molecular docking study revealed that the scFv 6B6 binds to an internal domain of Tc323. Immunofluorescence microscopy and Western Blot showed that Tc323 is expressed in the main developmental forms of T. cruzi, localized intracellularly and exhibiting a membrane-associated pattern. According to phylogenetic analysis, Tc323 is highly conserved throughout evolution in all the lineages of T. cruzi so far identified, but it is absent in Leishmania spp. and Trypanosoma brucei. Most interestingly, only plasma samples from patients infected with T. cruzi and those with mixed infection with Leishmania spp. reacted against Tc323. Collectively, our findings demonstrate that Tc323 is a promising candidate for the differential serodiagnosis of chronic Chagas disease in areas where T. cruzi and Leishmania spp. infections coexist.

Type II mode of JAK2 inhibition and destabilization are potential therapeutic approaches against the ruxolitinib resistance driven myeloproliferative neoplasms.

Ruxolitinib has been approved by the US FDA for the treatment of myeloproliferative neoplasms such as polycythemia vera and primary myelofibrosis. Ruxolitinib will remain a main stay in the treatment of MPN patients due to its effective therapeutic benefits. However, there have been instances of ruxolitinib resistance in MPN patients. As JAK2 is a direct target of ruxolitinib, we generated ruxolitinib-resistant clones to find out the mechanism of resistance. Cell-based screening strategy was used to detect the ruxolitinib-resistant mutations in JAK2. The Sanger sequencing method was used to detect the point mutations in JAK2. Mutations were re-introduced using the site-directed mutagenesis method and stably expressed in Ba/F3 cells. Drug sensitivities against the JAK2 inhibitors were measured using an MTS-based assay. JAK2 and STAT5 activation levels and total proteins were measured using immunoblotting. Computational docking studies were performed using the Glide module of Schrodinger Maestro software. In this study, we have recovered seven residues in the kinase domain of JAK2 that affect ruxolitinib sensitivity. All these mutations confer cross-resistance across the panel of JAK2 kinase inhibitors except JAK2-L983F. JAK2-L983F reduces the sensitivity towards ruxolitinib. However, it is sensitive towards fedratinib indicating that our screen identifies the drug-specific resistance profiles. All the ruxolitinib-resistant JAK2 variants displayed sensitivity towards type II JAK2 inhibitor CHZ-868. In this study, we also found that JAK1-L1010F (homologous JAK2-L983F) is highly resistant towards ruxolitinib suggesting the possibility of JAK1 escape mutations in JAK2-driven MPNs and JAK1 mutated ALL. Finally, our study also shows that HSP90 inhibitors are potent against ruxolitinib-resistant variants through the JAK2 degradation and provides the rationale for clinical evaluation of potent HSP90 inhibitors in genetic resistance driven by JAK2 inhibitors. Our study identifies JAK1 and JAK2 resistance variants against the type I JAK2 inhibitors ruxolitinib, fedratinib, and lestaurtinib. The sensitivity of these resistant variants towards the type II JAK2 inhibitor CHZ-868 indicates that this mode of type II JAK2 inhibition is a potential therapeutic approach against ruxolitinib refractory leukemia. This also proposes the development of potent and specific type II JAK2 inhibitors using ruxolitinib-resistance variants as a prototype.

Synthesis, computational docking and molecular dynamics studies of a new class of spiroquinoxalinopyrrolidine embedded chromanone hybrids as potent anti-cholinesterase agents.

Novel structurally intriguing heterocycles embedded with spiropyrrolidine, quinoxaline and chromanone units were synthesized in good yields using a [Bmim]Br accelerated multicomponent reaction strategy. The key step of the reaction is 1,3-dipolar cycloaddition involving highly functionalized dipolarophile, viz. 3-benzylidenechroman-4-one, to afford spiroquinoxalinopyrrolidine embedded chromanone hybrid heterocycles. The formation of spiro products occurs via two C-C, two N-C and one C-N bonds possessing four adjoining stereogenic centers, two of which are spiro carbons. The newly synthesized spiro compounds showed potent acetylcholinesterase and butyrylcholinesterase inhibitory activities. Moreover, compounds with fluorine displayed the highest AChE (3.20 ± 0.16 μM) and BChE (18.14 ± 0.06 μM) inhibitory activities. Further, docking studies, followed by all-atom molecular dynamics, showed results that are consistent with in vitro experimental findings. Although docking scores for the synthesized derivatives were higher than those of the standard drug, MD MMPBSA results showed better binding of synthesized derivatives (-93.5 ± 11.9 kcal mol-1) compared to the standard drug galantamine (-66.2 ± 12.3 kcal mol-1) for AChE but exhibited similar values (-98.1 ± 11.2 and -97.9 ± 11.5 kcal mol-1) for BChE. These differences observed in drug binding with AChE/BChE are consistent with RMSD, RMSF, LIG plots, and FEL structural analysis. Taken together, these derivatives could be potential candidates as inhibitors of AChE and BChE.

Antifungal potential of mannopyranoside derivatives through computational and molecular docking studies against Candida albicans 1IYL and 1AI9 proteins

Methyl α-D-mannopyranoside (MAM) is a naturally occurring carbohydrate derivative that has gained attention in drug discovery due to its potential therapeutic applications, particularly as an antifungal agent. In this study, we employed a computational approach to investigate the interactions between MAM and two Candida albicans antifungal proteins, 1IYL and 1AI9, through molecular docking simulations. Furthermore, we performed a PASS (Prediction of Activity Spectra for Substances) analysis to predict MAM potential biological activities, explored the pharmacokinetic properties and ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiles, and optimized the MAM using the density functional theory (DFT) method. The molecular docking results revealed favorable binding interactions between MAM and the active sites of the 1IYL and 1AI9 proteins, suggesting potential antifungal activity. Additionally, the ADMET profiles indicated low toxicity and suitable drug-like properties, such as moderate metabolic stability and minimal risk of adverse effects. Furthermore, DFT optimization was performed to investigate the molecular geometry and electronic properties of MAM. The optimization results provided valuable information on the stability and reactivity of MAM, enabling a better understanding of its chemical behavior and potential modifications for enhanced activity. Finally, PASS prediction was employed to evaluate MAM's potential biological activities beyond its antifungal properties. The analysis revealed several potential activities, including antibacterial, antiviral, and immunomodulatory effects, expanding the scope for future research and therapeutic applications. In conclusion, this computational study sheds light on the molecular interactions, pharmacokinetic properties, ADMET profiles, DFT optimization, and PASSES predictions of MAM. These findings highlight the potential of MAM as a promising antifungal agent with favorable pharmacological properties.

In silico and in vitro assessment of the anti-β-amyloid aggregation and anti-cholinesterase activities of Ptaeroxylon obliquum and Bauhinia bowkeri extracts

BackgroundAlzheimer’s disease (AD) is the most common form of dementia and dementia constitutes the fifth leading cause of mortality across the globe. Available treatment modalities and drugs have abysmally failed to curtail AD. This study evaluated the mitigation of Aβ aggregation and anti-cholinesterase activities with the crude extracts of Ptaeroxylon obliquum and Bauhinia bowkeri. Computational studies of the most abundant phytochemicals from the crude extracts of both plants with proteins were investigated. The phytochemical composition of the different crude extracts (hexane, DCM, and ethanol) of the plants were analyzed with FTIR and GC-MS. The inhibitory potential of the extracts on BACE-1 and cholinesterase activities was determined with both computational molecular docking studies and in vitro enzyme assays. Their anti-aggregation properties were confirmed with Thioflavin-T assay and TEM. ResultsThe in silico studies revealed that though thunbergol and cyclotetradecatriene (the major constituents of the extracts) inhibited all the proteins, the latter exhibited the best inhibitory potential. The in vitro results showed that while the dichloromethane (DCM) extract of P. obliquum had the highest butyrylcholinesterase (BuChE) inhibitory activity (1.77 µg/ml), the hexane and ethanol extract of B. bowkeri exhibited the highest β-site amyloid precursor cleaving enzymes-1 (BACE-1) (30.4 µg/ml) and acetylcholinesterase (AChE) (58.11 µg/ml) inhibitory efficacy, respectively. The ethanol extract (160 μg/ml) of B. bowkeri had the most efficacious anti-aggregation activity. ConclusionsThis study suggests that the plants could possess neuroprotective effects and could also be sources of anti-AD novel drugs.How to cite: Ojo MC, Mosa RA, Osunsanmi FO, et al. In silico and in vitro assessment of the anti-β-amyloid aggregation and anti-cholinesterase activities of Ptaeroxylon obliquum and Bauhinia bowkeri extracts. Electron J Biotechnol 2024;68. https://doi.org/10.1016/j.ejbt.2023.11.004.

In silico antibacterial, anticancer, antioxidant, antidiabetic activity predictions of the dual organic peroxide 2,5-dimethyl-2,5-di(tert-butyl peroxyl)hexane

In this search organic peroxide has been studied for its potential biological activities in various fields, including medicine and biotechnology. Molecular docking studies have been conducted to predict the binding between organic peroxide and certain biological targets, such as the breast cancer receptor 3hb5-oxidoreductase and the prostate cancer mutant 2q7k-Hormone. The docking results indicate potential interactions between peroxide and these targets. In addition to its potential cytotoxic activity, organic peroxide has been investigated for its antidiabetic activity. The docking results suggest that peroxide binds to the active site of enzymes involved in diabetes, such as α-amylase, pancreatic lipase, and β-glucosidase, with low binding energies. This indicates a potential role for peroxide in the treatment of diabetes. Furthermore, the interaction between peroxide and the antioxidant protein IHD2 (2HCK) has been explored. These computational studies suggest a possible pharmacological role for peroxide in the treatment of Helicobacter pylori (H. pylori) infection. The docking energy between peroxide and Helicobacter pylori adhesin HopQ type I bound to the N-terminal domain of human CEACAM1 indicates that peroxide could be a potential target to inhibit H. pylori infection. It’s important to note that these findings are based on computational methods and molecular docking studies. Further research, including in vitro and in vivo experiments, would be necessary to validate these findings and fully understand the potential benefits and limitations of peroxide in these applications.

Design, Synthesis, and Structure-Activity Relationship Studies of Novel GPR88 Agonists (4-Substituted-phenyl)acetamides Based on the Reversed Amide Scaffold.

The development of synthetic agonists for the orphan receptor GPR88 has recently attracted significant interest, given the promise of GPR88 as a novel drug target for psychiatric and neurodegenerative disorders. Examination of structure-activity relationships of two known agonist scaffolds 2-PCCA and 2-AMPP, as well as the recently resolved cryo-EM structure of 2-PCCA-bound GPR88, led to the design of a new scaffold based on the "reversed amide" strategy of 2-AMPP. A series of novel (4-substituted-phenyl)acetamides were synthesized and assessed in cAMP accumulation assays as GPR88 agonists, which led to the discovery of several compounds with better or comparable potencies to 2-AMPP. Computational docking studies suggest that these novel GPR88 agonists bind to the same allosteric site of GPR88 that 2-PCCA occupies. Collectively, our findings provide structural insight and SAR requirement at the allosteric site of GPR88 and a new scaffold for further development of GPR88 allosteric agonists.

Antioxidant, α-amylase and acetylcholinesterase inhibitory potential of Mazus pumilus (Japanese Mazus) extract: An in-vitro and in-silico study

Plant-derived secondary metabolites possess diverse biological activities that are beneficial to humans. Modern medications used for diabetes and Alzheimer’s often cause side effects, prompting reliance on traditional alternatives. Therefore, we aimed to uncover the potential of Mazus pumilus in countering diabetes and Alzheimer’s by in-vitro inhibition of α-amylase and AChE. Additionally, antioxidant activity and phytochemical analyses were performed. Mazus pumilusThe plant was extracted sequentially using n-hexane, ethyl acetate, dichloromethane, methanol, and water. The methanolic fraction, notably, manifested marked antioxidant efficacy against DPPH and ABTS radicals. Subsequently, this extract evinces noteworthy inhibitory attributes against α-amylase and AChE, respectively, in a competitive manner. Moreover, the bioactive phytoconstituents present in the methanolicextracts were determined through GC–MS analysis, and subsequent computational molecular docking studies revealed that these compounds strongly bound to the active site of both α-amylase and AChE. The calculated least binding energies, for α-amylase and AChE, underscore the viability of the molecular interactions. In conclusion, the antioxidant, antidiabetic, and anti-Alzheimer attributes of Mazus pumilus extract likely emanate from the synergistic interplay of its bioactive phytoconstituents. A comprehensive in-vitro and in-vivo study is essential to fully explore the anti-diabetic and anti-Alzheimer potential of secondary metabolites of Mazus pumilus.

Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2.

The mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays, and mass spectrometry analyses, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with the tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identify a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interactions with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs reveal that the interaction is conserved across mammalian species. In vitro kinase assays show that TBEV and LIV NS5 reduce the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response.