Silico Screening Research Articles

In Silico Screening of Metal-Organic Frameworks for Formaldehyde Capture with and without Humidity by Molecular Simulation.

Capturing formaldehydes (HCHO) from indoor air with porous adsorbents still faces challenges due to their low capacity and poor selectivity. Metal-organic frameworks (MOFs) with tunable pore properties were regarded as promising adsorbents for HCHO removal. However, the water presence in humid air heavily influences the formaldehyde capture performance due to the competition adsorption. To find suitable MOFs for formaldehyde capture and explore the relationship between MOFs structure and performance both in dry air and humid air, we performed grand canonical Monte Carlo (GCMC) molecular simulations to obtain working capacity and selectivity that evaluated the HCHO capture performance of MOFs without humidity. The results reveal that small pore size (~5 Å) and moderate heat of adsorption (40-50 kJ/mol) are favored for HCHO capture without water. It was found that the structure with a 3D cage instead of a 2D channel benefits the HCHO adsorption. Atoms in these high-performing MOFs should possess relatively small charges, and large Lennard-jones parameters were also preferred. Furthermore, it was indicated that Henry's constant (KH) can reflect the HCHO adsorption performance without humidity, in which the optimal range is 10-2-101. Hence, Henry's constant selectivity of HCHO over water (SKH HCHO/H2O) and HCHO over mixture components (H2O, N2, and O2) was obtained to screen MOFs at an 80% humidity condition. It was suggested that SKH for the mixture component overestimates the influence of N2 and O2, in which the top structures absorb a quantity of water in GCMC simulation, while SKH HCHO/H2O can efficiently find high-performing MOFs for HCHO capture at humidity in low adsorption pressure. The ECATAT found in this work has 0.64 mol/kg working capacity, and barely adsorbs water during 0-1 bar, which is the promising candidate MOF for HCHO capture.

High-Mobility Naphthalene Diimide Derivatives Revealed by Raman-Based In Silico Screening.

Charge transport in crystalline organic semiconductors (OSCs) is considerably hindered by low-frequency vibrations introducing dynamic disorder in the charge transfer integrals. Recently, we have shown that the contributions of various vibrational modes to the dynamic disorder correlate with their Raman intensities and suggested a Raman-based approach for estimation of the dynamic disorder and search for potentially high-mobility OSCs. In the present paper, we showcase this approach by revealing the highest-mobility OSC(s) in two series of crystalline naphthalene diimide derivatives bearing alkyl or cycloalkyl substituents. In contrast to our previous studies, Raman spectra are not measured, but are instead calculated using periodic DFT. As a result, an OSC with a potentially high charge mobility is revealed in each of the two series, and further mobility calculations corroborate this choice. Namely, for the naphthalene diimide derivatives with butyl and cyclopentyl substituents, the estimated room-temperature isotropic electron mobilities are as high as 6 and 15 cm2 V-1 s-1, respectively, in the latter case even exceeding 20 cm2 V-1 s-1 in a two-dimensional plane. Thus, our results highlight the potential of using the calculated Raman spectra to search for high-mobility crystalline OSCs and reveal two promising OSCs, which were previously overlooked.

Synthesis, Biocidal and Antibiofilm Activities of New Isatin-Quinoline Conjugates against Multidrug-Resistant Bacterial Pathogens along with Their In Silico Screening.

Isatin-quinoline conjugates 10a-f and 11a-f were assembled by the reaction of N-(bromobutyl) isatin derivatives 3a, b with aminoquinolines 6a-c and their corresponding hydrazinyl 9a-c in good yields. The structures of the resulting conjugates were established by spectroscopic tools and showed data consistent with the proposed structures. In vitro antibacterial activity against different bacterial strains was evaluated. All tested conjugates showed significant biocidal activity with lower MIC than the first line drugs chloramphenicol and ampicillin. Conjugates 10a, 10b and 10f displayed the most potent activity against all clinical isolates. The antibiofilm activity for all tested conjugates was screened against the reference drug vancomycin using the MRSA strain. The results revealed that all conjugates had an inhibitory activity against biofilm formation and conjugate. Conjugate 11a showed 83.60% inhibition at 10 mg/mL. In addition, TEM studies were used to prove the mechanism of antibacterial action of conjugates 10a and 11a against (MRSA). Modeling procedures were performed on 10a-f and 11a-f and interestingly the results were nearly consistent with the biological activities. In addition, in silico pharmacokinetic evaluation was performed and revealed that the synthesized compounds 10a-f and 11a-f were considered drug-like molecules with promising bioavailability and high GI absorption. The results confirmed that the title compounds caused the disruption of bacterial cell membranes and could be used as potential leads for the further development and optimization of antibacterial agents.

In Silico Screening of Active Compounds in Garri for the Inhibition of Key Enzymes Linked to Diabetes Mellitus

Through in silico screening, this study seeks to demonstrate a connection between ethnopharmacological claims and the bioactive components found in Garri against potential targets for diabetes. The process of molecular docking involving different bonding modes of compounds in Garri with active cavities of target receptors for proteins human pancreatic alpha-amylase (HPA) and human lysosomal acid-alpha-glucosidase (GAA) was carried out in autodock vina. Density functional theory was used for quantum chemical analysis, while ADME/T properties of the top binding compounds were predicted using the Admetsar and Swissadme database. From the results, (20E)-6-hydroxycholesta-9(11),20(22)-diene-3,23-dione, 25-dedhydrotigogenin, cochlioquinone B, and psi-diosgenin, showed the best docking results (> −8.1 to −9.8 kcal/mol), when compared with the standard control drugs acarbose (−7.9 kcal/mol) and 1-deoxynojirimycin (< −5.1 kcal/mol). The results from the ADME/T prediction also revealed that the compounds had good pharmacokinetic properties. The study provided insights into the development of better inhibitors to treat diabetes from garri.

Structure Based in Silico Screening Revealed a Potent Acinetobacter Baumannii Ftsz Inhibitor From Asinex Antibacterial Library.

The superbug Acinetobacter baumannii is an increasingly prevalent pathogen of the intensive care units where its treatment is challenging. The identification of newer drug targets and the development of propitious therapeutics against this pathogen is of utmost importance. A drug target, cell division enzyme (FtsZ), involved in A. baumannii cytokinesis is a promising avenue for antibacterial therapy. Structure based virtual screening illustrated a lead-like molecule from Asinex antibacterial library to have the best binding affinity for the FtsZ active pocket. Computational pharmacokinetics predicted the compound to have the safest pharmacokinetics profile, thus maximizing the chances of the molecule reaching the market with enhanced efficacy and lesser toxicity. Molecular dynamics simulations in an aqueous environment revealed the flexibility of protein loop regions, and upward extension followed by the backward movement of the inhibitor N, N-dimethylpyridazin-3-amine ring on its axis. The active pocket residue Thr310 demonstrated to play significant role in inhibitor binding. The binding free energy predicted by MM/GBSA and MM/PBSA reflected system stability with a total value of -62.15 kcal/mol and -10.60 kcal/mol, respectively. The absolute binding free energy estimated by WaterSwap was -16 kcal/mol that validates and affirms complex stability. The inhibitor represents a promising scaffold as a lead optimization for the FtsZ enzyme.

In Vitro and In Silico Screening of Anti-Vibrio spp., Antibiofilm, Antioxidant and Anti-Quorum Sensing Activities of Cuminum cyminum L. Volatile Oil.

Cuminum cyminum L. essential oil (cumin EO) was studied for its chemical composition, antioxidant and vibriocidal activities. Inhibition of biofilm formation and secretion of some virulence properties controlled by the quorum sensing system in Chromobacterium violaceum and Pseudomonas aeruginosa strains were also reported. The obtained results showed that cuminaldehyde (44.2%) was the dominant compound followed by β-pinene (15.1%), γ-terpinene (14.4%), and p-cymene (14.2%). Using the disc diffusion assay, cumin EO (10 mg/disc) was particularly active against all fifteen Vibrio species, and the highest diameter of growth inhibition zone was recorded against Vibrio fluvialis (41.33 ± 1.15 mm), Vibrio parahaemolyticus (39.67 ± 0.58 mm), and Vibrio natrigens (36.67 ± 0.58 mm). At low concentration (MICs value from 0.023–0.046 mg/mL), cumin EO inhibited the growth of all Vibrio strains, and concentrations as low as 1.5 mg/mL were necessary to kill them (MBCs values from 1.5–12 mg/mL). Using four antioxidant assays, cumin EO exhibited a good result as compared to standard molecules (DPPH = 8 ± 0.54 mg/mL; reducing power = 3.5 ± 0.38 mg/mL; β-carotene = 3.8 ± 0.34 mg/mL; chelating power = 8.4 ± 0.14 mg/mL). More interestingly, at 2x MIC value, cumin EO inhibited the formation of biofilm by Vibrio alginolyticus (9.96 ± 1%), V. parahaemolyticus (15.45 ± 0.7%), Vibrio cholerae (14.9 ± 0.4%), and Vibrio vulnificus (18.14 ± 0.3%). In addition, cumin EO and cuminaldehyde inhibited the production of violacein on Lauria Bertani medium (19 mm and 35 mm, respectively). Meanwhile, 50% of violacein inhibition concentration (VIC50%) was about 2.746 mg/mL for cumin EO and 1.676 mg/mL for cuminaldehyde. Moreover, elastase and protease production and flagellar motility in P. aeruginosa were inhibited at low concentrations of cumin EO and cuminaldehyde. The adopted in-silico approach revealed good ADMET properties as well as a high binding score of the main compounds with target proteins (1JIJ, 2UV0, 1HD2, and 3QP1). Overall, the obtained results highlighted the effectiveness of cumin EO to prevent spoilage with Vibrio species and to interfere with the quorum sensing system in Gram-negative bacteria by inhibiting the flagellar motility, formation of biofilm, and the secretion of some virulence enzymes.

In Vitro Evaluation of In Silico Screening Approaches in Search for Selective ACE2 Binding Chemical Probes.

New models for ACE2 receptor binding, based on QSAR and docking algorithms were developed, using XRD structural data and ChEMBL 26 database hits as training sets. The selectivity of the potential ACE2-binding ligands towards Neprilysin (NEP) and ACE was evaluated. The Enamine screening collection (3.2 million compounds) was virtually screened according to the above models, in order to find possible ACE2-chemical probes, useful for the study of SARS-CoV2-induced neurological disorders. An enzymology inhibition assay for ACE2 was optimized, and the combined diversified set of predicted selective ACE2-binding molecules from QSAR modeling, docking, and ultrafast docking was screened in vitro. The in vitro hits included two novel chemotypes suitable for further optimization.

In Silico Screening of Two‐Photon Absorption Properties of a Large Set of Bis‐Difluoroborate Dyes

AbstractIn this work we strive to unravel the relationships between the two‐photon absorption (2PA) cross‐sections and structural modifications in an extended panel (280 compounds) of large difluoroborate dyes. More specifically, we use theoretical tools based on Time‐Dependent Density Functional Theory (TD‐DFT), to predict the one and two‐photon absorption properties of all compounds. The BF2‐carrying dyes usually posses a great interest for 2PA bioapplications as smartly designed BF2‐derivatives show good photophysical properties and high quantum yields in aqueous medium. For practical applications, it is important to maximize their 2PA response as well as absorption wavelength. This is why we explore here various strategies for maximizing the 2PA cross‐section: core modifications, multi‐branching, variation of the nature and length of the π‐conjugated linkers, addition of various donor and acceptor substituents. Our results suggest that large values of 2PA cross‐section and redshifted absorption wavelength can be achieved for all studied cores by using the vinylene‐type linkers and asymmetrical substitution with at least one strong peripheral donor group.

Discovery of New Inhibitors of eEF2K from Traditional Chinese Medicine Based on In Silico Screening and In Vitro Experimental Validation.

Eukaryotic elongation factor 2 kinase (eEF2K) is a highly conserved α kinase and is increasingly considered as an attractive therapeutic target for cancer as well as other diseases. However, so far, no selective and potent inhibitors of eEF2K have been identified. In this study, pharmacophore screening, homology modeling, and molecular docking methods were adopted to screen novel inhibitor hits of eEF2K from the traditional Chinese medicine database (TCMD), and then cytotoxicity assay and western blotting were performed to verify the validity of the screen. Resultantly, after two steps of screening, a total of 1077 chemicals were obtained as inhibitor hits for eEF2K from all 23,034 compounds in TCMD. Then, to verify the validity, the top 10 purchasable chemicals were further analyzed. Afterward, Oleuropein and Rhoifolin, two reported antitumor chemicals, were found to have low cytotoxicity but potent inhibitory effects on eEF2K activity. Finally, molecular dynamics simulation, pharmacokinetic and toxicological analyses were conducted to evaluate the property and potential of Oleuropein and Rhoifolin to be drugs. Together, by integrating in silico screening and in vitro biochemical studies, Oleuropein and Rhoifolin were revealed as novel eEF2K inhibitors, which will shed new lights for eEF2K-targeting drug development and anticancer therapy.

In Silico Screening of Quorum Sensing Inhibitor Candidates Obtained by Chemical Similarity Search.

Quorum sensing (QS) is a bacterial communication using signal molecules, by which they sense population density of their own species, leading to group behavior such as biofilm formation and virulence. Autoinducer-2 (AI2) is a QS signal molecule universally used by both gram-positive and gram-negative bacteria. Inhibition of QS mediated by AI2 is important for various practical applications, including prevention of gum-disease caused by biofilm formation of oral bacteria. In this research, molecular docking and molecular dynamics (MD) simulations were performed for molecules that are chemically similar to known AI2 inhibitors that might have a potential to be quorum sensing inhibitors. The molecules that form stable complexes with the AI2 receptor protein were found, suggesting that they could be developed as a novel AI2 inhibitors after further in vitro validation. The result suggests that combination of ligand-based drug design and computational methods such as MD simulation, and experimental verification, may lead to development of novel AI inhibitor, with a broad range of practical applications.

In Silico Screening of Schistosome Membrane Proteins as Candidate Diagnostic Antigens for Asian Schistosomiasis

Asian schistosomiasis is primarily caused by Schistosoma japonicum. Given the relatively low prevalence of the disease, efforts are now focused on its elimination. However, the low sensitivity of the current diagnostic techniques underestimates the actual prevalence of schistosomiasis in areas with low endemicity. Therefore, this study aims to identify candidate diagnostic antigens that are potentially useful for the development of a reliable serological diagnosis of Asian schistosomiasis using the genomic databases of S. haematobium and S. japonicum. On the SchistoDB database, this study first employed a preliminary genomic filtration on 12,021 S. haematobium genes – including the presence of transmembrane domain, signal peptides, isoelectric point, and molecular weight yielding 113 genes. Further gene ontology (GO) enrichment analysis resulted in 22 candidate S. haematobium genes. These S. haematobium genes were then compared with the S. japonicum genome in the WormBase ParaSite, identifying 36 S. japonicum homologous proteins. The amino acid sequences of the 36 proteins were aligned using ClustalW to identify identical proteins, resulting in 21 distinct S. japonicum proteins considered as the final set of candidate diagnostic antigens. Therefore, these 21 candidate diagnostic antigens can be useful in developing a reliable serological diagnosis of Asian schistosomiasis, which may be accomplished through in vitro validation, protein characterization, and serological evaluation.

In Silico Screening and Development of Microsatellite Markers for Genetic Analysis in Perca fluviatilis.

Simple SummaryPerca fluviatilis is an economically important species of freshwater fish that has flavorsome meat with a high nutritional value. Microsatellite markers are widely used in the genetic structure analysis of aquatic animals due to their abundance, high polymorphism, and codominance. In this study, we screened, tested, and developed polymorphic markers and evaluated the genetic diversity of the main wild P. fluviatilis populations in China. From the P. fluviatilis genomic data, 98,425 pairs of microsatellites were identified. A total of 200 primer pairs for tetranucleotide microsatellites were synthesized and tested in randomly selected wild individuals. Among them, 152 microsatellite markers were found to be polymorphic. A total of 29 markers with clear amplified bands and high polymorphism were selected for the genetic analysis of the four populations. The results indicated a high level of genetic diversity in P. fluviatilis populations in Wulungu Lake, Jili Lake, and the Wulungu River and a medium level of genetic diversity in the Kalaeerqisi River. There was moderate genetic differentiation among the populations in Xinjiang. The results of this study provide important information on the genetic diversity and genetic population structuring of P. fluviatilis in China as well as a scientific basis for the protection and molecular marker-assisted breeding of P. fluviatilis.Perca fluviatilis is an economically important species of freshwater fish. To understand the genetic structure of P. fluviatilis in China, 268 samples were collected from Wulungu Lake (WL), Jili Lake (JL), the Wulungu River (WR), and the Kalaeerqisi River (KR). These samples were then analyzed using microsatellite markers. A total of 98,425 microsatellite markers were developed based on the genomic data, and 29 polymorphic microsatellite markers were selected to analyze genetic diversity in this study. The number of alleles (Na) and observed heterozygosity (Ho) per population ranged from 4.621 (KR) to 11.172 (WL) and from 0.510 (KR) to 0.716 (JL), respectively. The results of the polymorphic information content (PIC) showed that the WL, JL, and WR populations were highly polymorphic (PIC ≥ 0.5) and that the KR population was moderately polymorphic (0.25 ≤ PIC < 0.5). The genetic differentiation coefficient (Fst) among the four P. fluviatilis populations was 0.074, indicating moderate genetic differentiation among the populations in Xinjiang. The reason for the significant difference between the rivers and lakes could be the presence of a dam blocking the flow of P. fluviatilis. The development of microsatellite markers provides support for population genetics in the future. The evaluation of the genetic structure of P. fluviatilis in Xinjiang provides a reference for the reproduction and conservation of P. fluviatilis.

In Silico Screening of Novel TMPRSS2 Inhibitors for Treatment of COVID-19.

COVID-19, a pandemic caused by the virus SARS-CoV-2, has spread globally, necessitating the search for antiviral compounds. Transmembrane protease serine 2 (TMPRSS2) is a cell surface protease that plays an essential role in SARS-CoV-2 infection. Therefore, researchers are searching for TMPRSS2 inhibitors that can be used for the treatment of COVID-19. As such, in this study, based on the crystal structure, we targeted the active site of TMPRSS2 for virtual screening of compounds in the FDA database. Then, we screened lumacaftor and ergotamine, which showed strong binding ability, using 100 ns molecular dynamics simulations to study the stability of the protein–ligand binding process, the flexibility of amino acid residues, and the formation of hydrogen bonds. Subsequently, we calculated the binding free energy of the protein–ligand complex by the MM-PBSA method. The results show that lumacaftor and ergotamine interact with residues around the TMPRSS2 active site, and reached equilibrium in the 100 ns molecular dynamics simulations. We think that lumacaftor and ergotamine, which we screened through in silico studies, can effectively inhibit the activity of TMPRSS2. Our findings provide a basis for subsequent in vitro experiments, having important implications for the development of effective anti-COVID-19 drugs.

In Silico Screening and Testing of FDA-Approved Small Molecules to Block SARS-CoV-2 Entry to the Host Cell by Inhibiting Spike Protein Cleavage.

The COVID-19 pandemic began in 2019, but it is still active. The development of an effective vaccine reduced the number of deaths; however, a treatment is still needed. Here, we aimed to inhibit viral entry to the host cell by inhibiting spike (S) protein cleavage by several proteases. We developed a computational pipeline to repurpose FDA-approved drugs to inhibit protease activity and thus prevent S protein cleavage. We tested some of our drug candidates and demonstrated a decrease in protease activity. We believe our pipeline will be beneficial in identifying a drug regimen for COVID-19 patients.

In Silico Screening of Synthetic and Natural Compounds to Inhibit the Binding Capacity of Heavy Metal Compounds against EGFR Protein of Lung Cancer.

Inorganic pollutant, specifically heavy metals' contamination, is a significant matter of concern and is one of the key contributors in various health disorders including cancer. However, the interaction of heavy metals (HMs) with lung cancer has rarely been explored yet. Therefore, the present study was intended with the aim to identify the interactions of HMs with the target protein “epidermal growth factor receptor (EGFR)” of lung cancer and explore potential drug candidates, which could inhibit the active site of EGFR against HM exposure. The molecular operating environment (MOE) tool was used to study the interactions of HMs with EGFR protein. The drug-drug interaction (DDI) network approach was used to identify the potential drug candidates, which were further confirmed and compared with the commercial medicines/control group. Various compounds of twenty-three HMs were docked with EGFR protein. Out of which tinidazole, thallium bromodimethyl, and silver acetate (Sn, Ti, and Ag compounds) showed strong interactions with EGFR based on lowest-scoring values (-20.42, -7.86, and -7.74 kcal/mol, respectively). Among 1280 collected drug candidates, three synthetic compounds viz., ZINC00602803, ZINC00602685, and ZINC06718468 and three natural compounds (berberine chloride, transresveratrol, and ellagic acid) depicted strong binding capacity with EGFR. Specifically, the scoring value of ZINC00602803 (-30.99 kcal/mol) was even lowest than standard lung cancer drugs (afatinib, erlotinib, and gefitinib). Our findings revealed that both natural and synthetic compounds having strong associations with EGFR protein could be potential candidates to inhibit the interaction between HMs and lung cancer protein and can also be used as an alternative for the prevention and treatment of lung cancer. However, in vitro and in vivo studies should be conducted to validate the aforementioned natural and synthetic compounds.

In Silico Screening and Validation of PDGFRA Inhibitors Enhancing Radioiodine Sensitivity in Thyroid Cancer

Aberrant activation of platelet-derived growth factor receptor α (PDGFRA) has been implicated in tumorigenesis and radioiodine resistance of thyroid cancer, indicating its therapeutic potential. In the present study, we confirmed the association between PDGFRA and radioiodine resistance in thyroid cancer using bioinformatics analysis and constructed a prediction model of PDGFRA inhibitors using machine learning and molecular docking approaches. We then performed a virtual screening of a traditional Chinese medicine (TCM) derived compound library and successfully identified 4’,5,7-trimethoxyflavone as a potential PDGFRA inhibitor. Further characterization revealed a significant inhibitory effect of 4’,5,7-trimethoxyflavone on PDGFRA-MAPK pathway activation, and that it could upregulate expression of sodium iodide symporter (NIS) as well as improve radioiodine uptake capacity of radioiodine-refractory thyroid cancer (RAIR-TC), suggesting it a potential drug lead for the development of new RAIR-TC therapy.

In Silico Screening of Natural Compounds for Candidates 5HT6 Receptor Antagonists against Alzheimer's Disease.

Alzheimer’s disease (AD), a devastating neurodegenerative disease, is the focus of pharmacological research. One of the targets that attract the most attention for the potential therapy of AD is the serotonin 5HT6 receptor, which is the receptor situated exclusively in CNS on glutamatergic and GABAergic neurons. The neurochemical impact of this receptor supports the hypothesis about its role in cognitive, learning, and memory systems, which are of critical importance for AD. Natural products are a promising source of novel bioactive compounds with potential therapeutic potential as a 5HT6 receptor antagonist in the treatment of AD dementia. The ZINC—natural product database was in silico screened in order to find the candidate antagonists of 5-HT6 receptor against AD. A virtual screening protocol that includes both short-and long-range interactions between interacting molecules was employed. First, the EIIP/AQVN filter was applied for in silico screening of the ZINC database followed by 3D QSAR and molecular docking. Ten best candidate compounds were selected from the ZINC Natural Product database as potential 5HT6 Receptor antagonists and were proposed for further evaluation. The best candidate was evaluated by molecular dynamics simulations and free energy calculations.

Photoexcited Intramolecular Charge Transfer in Dye Sensitizers: Predictive In Silico Screening for Dye-Sensitized Solar Cell Devices.

Efficient photoinduced intramolecular charge transfer (ICT) from donor to acceptor in dye molecules is the functional basis and key property in the working of a dye-sensitized solar cell (DSSC). To understand the ICT process in photoexcited dye molecules, we analyze the electronic properties and structural parameters of a chosen set of experimentally synthesized donor–acceptor (D–A) and donor−π-spacer−acceptor (D−π–A) type dye molecules in their ground, excited, and cationic states. The correlation between structural modification and charge redistribution in different parts of the molecule helps to identify the extent of π-conjugation and spatial rearrangement of electron density localization along the molecular skeleton. We find that prominent twisting of several groups and the resulting molecular bond rearrangements in larger parts of the molecule promote efficient donor to acceptor ICT, such as in D–A type ADEKA1 and C275 dyes. Thus, based on the modest computation of structural and electronic properties of dye molecules in their respective ground, excited, and cationic states, we identify the desired structural changes that facilitate tunable intramolecular charge transfer to highlight a simple and direct prescription to screen out probable efficient dye molecules among many samples. Our approach complements recent experimental evidence of capturing the structural view of the excited-state charge transfer in molecules.

In Silico Screening of Cinnamon (Cinnamomum burmannii) Bioactive Compounds as Acetylcholinesterase Inhibitors

Alzheimer’s is a progressive and neurodegenerative disease that mainly affects people aged 65 years and older. The pathophysiology of Alzheimer’s is possibly related to the depletion of the neurotransmitter acetylcholine (ACh) due to beta-amyloid plaques and neurofibrillary tangles. Secondary metabolites found in cinnamon bark (Cinnamomum burmannii) have the potential as anticholinesterases to treat Alzheimer’s symptoms. This study aimed to identify the potency of bioactive compounds from cinnamon bark as AChE inhibitors in silico through analysis of binding energy, inhibition constants, and types of interactions. The research was conducted by screening virtually 60 test ligands using the PyRx program and molecular docking using the Autodock Tools program. The results of the ligand-receptor interaction analysis showed that 12 of the 15 tested ligands had potential as AChE inhibitors. Epicatechin and medioresinol are the ligands with the best potential for AChE inhibition with affinity close to the natural ligand or donepezil. Epicatechin has a binding energy of −10.0 kcal/mol and inhibition constant of 0.0459 M, with four hydrogen bonds and seven hydrophobic bonds. Meanwhile, medioresinol has −9.9 kcal/mol binding energy and inhibition constant of 0.0543 M, with one hydrogen bond and thirteen hydrophobic bonds.

Synthesis of Novel Derivatives of 5,6,7,8-Tetrahydroquinazolines Using α-Aminoamidines and In Silico Screening of Their Biological Activity.

α-Aminoamidines are promising reagents for the synthesis of a diverse family of pyrimidine ring derivatives. Here, we demonstrate the use of α-aminoamidines for the synthesis of a new series of 5,6,7,8-tetrahydroquinazolines by their reaction with bis-benzylidene cyclohexanones. The reaction occurs in mild conditions and is characterized by excellent yields. It has easy workup, as compared to the existing methods of tetrahydroquinazoline preparation. Newly synthesized derivatives of 5,6,7,8-tetrahydroquinazoline bear protecting groups at the C2-tert-butyl moiety of a quinazoline ring, which can be easily cleaved, opening up further opportunities for their functionalization. Moreover, molecular docking studies indicate that the synthesized compounds reveal high binding affinity toward some essential enzymes of Mycobacterial tuberculosis, such as dihydrofolate reductase (DHFR), pantothenate kinase (MtPanK), and FAD-containing oxidoreductase DprE1 (MtDprE1), so that they may be promising candidates for the molecular design and the development of new antitubercular agents against multidrug-resistant strains of the Tubercle bacillus. Finally, the high inhibition activity of the synthesized compounds was also predicted against β-glucosidase, suggesting a novel tetrahydroquinazoline scaffold for the treatment of diabetes.