Computational Docking Studies Research Articles

Highly Selective Drug-Derived Fluorescent Probes for the Cannabinoid Receptor Type 1 (CB1R).

The cannabinoid receptor type 1 (CB1R) is pivotal within the endocannabinoid system regulating various signaling cascades with effects in appetite regulation, pain perception, memory formation, and thermoregulation. Still, understanding of CB1R's cellular signaling, distribution, and expression dynamics is very fragmentary. Real-time visualization of CB1R is crucial for addressing these questions. Selective drug-like CB1R ligands with a defined pharmacological profile were investigated for the construction of CB1R fluorescent probes using a reverse design-approach. A modular design concept with a diethyl glycine-based building block as the centerpiece allowed for the straightforward synthesis of novel probe candidates. Validated by computational docking studies, radioligand binding, and cAMP assay, this systematic approach allowed for the identification of novel pyrrole-based CB1R fluorescent probes. Application in fluorescence-based target-engagement studies and live cell imaging exemplify the great versatility of the tailored CB1R probes for investigating CB1R localization, trafficking, pharmacology, and its pathological implications.

Design and evaluation of novel inhibitors for the treatment of clear cell renal cell carcinoma

The efficacy of conventional chemotherapies in treating clear cell renal cell carcinoma (ccRCC) is often limited due to its high molecular diversity, generally low response rates to standard treatments, and prevalent drug resistance. Recent advancements in the molecular understanding of ccRCC, alongside the discovery of novel therapeutic agents targeting specific proteins, have significantly altered the treatment landscape for ccRCC. Here, we synthesized 27 new compounds that are derivatives of TG-101209 to modulate BUB1B (BUB1 mitotic checkpoint serine/threonine kinase B). BUB1B has been recently identified as a drug target for the development of effective ccRCC treatment based on global transcriptomics profiling of ccRCC tumours and gene co-expression network analysis. We characterized the molecular structures of these 27 compounds by 1H and 13C NMR and Mass spectrometry. We evaluated the effect of these 27 compounds by analysing the modulation of the BUB1B expression. Our primary objective was to design and assess the efficacy of these new compounds in reducing the viability of Caki-1 cells, a ccRCC cell line. We performed the computational docking studies by the Schrödinger Maestro software and demonstrated that three of these compounds (13a, 5i, and 5j) effectively downregulated BUB1B expression and eventually triggered necrosis and apoptosis in the Caki-1 cell line based on the structure–activity relationship (SAR) analysis. The IC50 values for compounds 13a, 5i, and 5j were calculated as 2.047 µM, 10.046 µM, and 6.985 µM, respectively, indicating their potent inhibitory effects on cell viability. Our study suggests that these compounds targeting BUB1B could offer a more effective and promising approach for ccRCC treatment compared to the conventionally used tyrosine kinase inhibitors. Our study underscores the potential of leveraging targeted therapies against specific molecular pathways in ccRCC may open new avenues for the development of effective treatment strategies against ccRCC.

Revisiting the dipeptidyl carboxypeptidase inhibitor captopril as a source of pan anti-trypanosomatid agents

The protozoan parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. are responsible for continued propagation of neglected tropical diseases such as African sleeping sickness, Chagas disease and leishmaniasis respectively. Following a report that captopril targets Leishmania donovani dipeptidyl carboxypeptidase, a series of simple proline amides and captopril analogues were synthesized and found to exhibit 1–2 μM in vitro inhibition and selectivity against Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. The results were corroborated with computational docking studies. Arguably, the synthetic proline amides represent the structurally simplest examples of in vitro pan antiprotozoal compounds.

Ultrasound-Assisted Ring Opening of Epoxides in HFIP: THF: Synthesis, Characterization, Computational Studies and Molecular Docking of novel 2-hydroxy Dithiocarbamates

Under the influence of ultrasonic irradiation, pyridazinone, triazinone, or phthalimide containing 2-hydroxy dithiocarbamates, a biologically relevant novel organo-sulfur compound, was synthesized. Detailed characterization, computational, and molecular docking studies are being investigated. Molecular interactions were studied using 3D Hirshfeld surfaces and corresponding 2D fingerprint plots. Theoretical (DFT) studies on the molecular structure, HOMO, LUMO, and quantum chemical descriptors were performed at the B3LYP/6-311++G(dp) level of theory. At the same time, the interaction energy was computed using the B3LYP/6-31G(d,p) level of theory. The FMO study revealed that molecules 4a and 4p in the gas phase have 3.545 eV and 3.263 eV HOMO-LUMO energy gaps, respectively, and they are hence kinetically stable. Quantum chemical calculations confirm the electrophilic character of compounds 4a and 4p, as the molecule is stable and highly electrophilic. The interactions of 2-hydroxy dithiocarbamate derivatives (4a-4t) with the ligand-binding site of the target COX-2 (cyclooxygenase-2) enzyme were investigated using in-silico molecular docking experiments. Compared to the standard medicine celecoxib, the results showed that most synthesized derivatives had better glide scores and interaction. The docking study of all the synthesized compounds revealed that compounds 4a, 4e, and 4o interact well with the COX-2 enzyme as anti-inflammatory drugs. Molecular dynamic simulation was utilized to validate the docking study and explore the stable binding site and interaction of compound 4o, which is the most potent. The findings indicated that compound 4o exhibited better stability and interaction when compared to the reference drug.

Cannabidiol promotes intestinal cholesterol uptake mediated by Pregnane X receptor.

Cannabidiol (CBD), a non-psychoactive phytocannabinoid of cannabis, is therapeutically used as an analgesic, anti-convulsant, anti-inflammatory, and anti-psychotic drug. There is a growing concern about the adverse side effects posed by CBD usage. Pregnane X receptor (PXR) is a nuclear receptor activated by a variety of dietary steroids, pharmaceutical agents, and environmental chemicals. In addition to the role in xenobiotic metabolism, the atherogenic and dyslipidemic effects of PXR have been revealed in animal models. CBD has a low affinity for cannabinoid receptors, thus it is important to elucidate the molecular mechanisms by which CBD activates cellular signaling and to assess the possible adverse impacts of CBD on pro-atherosclerotic events in cardiovascular system, such as dyslipidemia. Our study aims to explore the cellular and molecular mechanisms by which exposure to CBD activates human PXR and increases the risk of dyslipidemia. Both human hepatic and intestinal cells were used to test if CBD was a PXR agonist via cell-based transfection assay. The key residues within PXR's ligand-binding pocket that CBD interacted with were investigated using computational docking study together with site-directed mutagenesis assay. The C57BL/6 wildtype mice were orally fed CBD in the presence of PXR antagonist resveratrol (RES) to determine how CBD exposure could change the plasma lipid profiles in a PXR-dependent manner. Human intestinal cells were treated with CBD and/or RES to estimate the functions of CBD in cholesterol uptake. CBD was a selective agonist of PXR with higher activities on human PXR than rodents PXRs and promoted the dissociation of human PXR from nuclear co-repressors. The key amino acid residues Met246, Ser247, Phe251, Phe288, Trp299, and Tyr306 within PXR's ligand binding pocket were identified to be necessary for the agonistic effects of CBD. Exposure to CBD increased the circulating total cholesterol levels in mice which was partially caused by the induced expression levels of the key intestinal PXR-regulated lipogenic genes. Mechanistically, CBD induced the gene expression of key intestinal cholesterol transporters, which led to the increased cholesterol uptake by intestinal cells. CBD was identified as a selective PXR agonist. Exposure to CBD activated PXR signaling and increased the atherogenic cholesterol levels in plasma, which partially resulted from the ascended cholesterol uptake by intestinal cells. Our study provides potential evidence for the future risk assessment of CBD on cardiovascular disease, such as dyslipidemia.

Exploring the uncharted territory of the potential protein-protein interactions of cytosolic malate dehydrogenase.

In this review, we examine the protein-protein interactions of cytosolic malate dehydrogenase (MDH), an under-studied area in cellular metabolism. We provide a comprehensive overview of MDH involvement in metabolism, especially its interactions with metabolic partners and dynamics of changing metabolism. We present an analysis of the biophysical nature of these interactions and the current methods used to study them. Our review includes an assessment of computational docking studies, which offer initial hypotheses about potential MDH interaction partners. Furthermore, we provide a summary of the sparse yet insightful experimental evidence available, establishing a foundation for future research. By integrating biophysical analysis and methodological advancements, this paper aims to illuminate the intricate network of interactions involving cytosolic MDH and their metabolic implications. This work not only contributes to our understanding of MDH's role in metabolism but also highlights the potential impact of these interactions in metabolic disorders.

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.

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.