Dynamics Simulation Study Research Articles

Deciphering the 4',7-Dihydroxy-3'-Methylflavone from Boerhavia, Agonist/Antagonist Interactions Against 5-HT2 Receptors using Homology Modeling, Molecular Docking, and Dynamic Simulation Studies.

Seizures, depression, and anxiety are neurological disorders that affected innumerable people worldwide. Recent research has revealed that targeting 5-hydroxytryptamine 2 (5-HT2) receptors can help suppress these conditions. An in-depth literature study has identified that phytocompounds from the Boerhavia genus could reduce seizures. Therefore, homology models of 5-HT2 receptors were generated and validated using techniques such as the alignment of amino acid sequences and the Ramachandran plot. Later, a comparison of modeled structures was made with a non-redundant set of PDB structures. The pharmacokinetics, drug-likeness, blood-brain barrier (BBB) permeability, and Lipinski's rule of five shed light on 22 phytocompounds, which are the potential candidates for molecular docking among 127 Boerhavia's bioactive. Notably, molecular docking analysis revealed 4',7-dihydroxy-3'-methylflavone as the most potent lead compound, which has a strong binding affinity to all modeled receptors. Additionally, with a remarkably high docking score of -9.1 kcal/mol, 4',7-dihydroxy-3'-methylflavone showed promising interactions, particularly with 5-HT2A receptor, as seen from the RMSD, SASA, Rg, and number of hydrogen bonds during 100 ns molecular dynamic (MD) simulation. Principal component analysis (PCA) and Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) further confirmed that 4',7-dihydroxy-3'-methylflavone is the best novel phytocompound in Boerhavia genus for 5-HT2 receptor as agonist/antagonist activity against seizures.

Artemisia campestris L. as a promising source of potential antiviral drugs for SARS-CoV-2: Docking and dynamic simulation studies

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been considered as global public health security threats. Due to its rapid spread, high mortality rate and unavailability of treatment, we need to find a potent drug against SARS-CoV-2. Natural products are useful agents for the discovery of new potential drugs to combat coronavirus. Artemisia campestris, an aromatic plant widely used in traditional medicine, particularly in southern region of Algeria, is recognized for its essential oils and phenolics compounds possessing a wide range of biological activities. This study selected sixty-nine compounds from this plant to determine their binding interactions with the SARS-CoV-2 main protease (Mpro) and receptor-binding domain of the spike (S-RBD) protein, by using computational methods. Rutin, isoquercetin, and quercetin-3-O-glucuronide were shown to be the most potent inhibitors for Mpro and S-RBD with docking scores and Ki values ranging from -16.06 to -10.67 Kcal/mol and 0.005 to 30.01 nM, respectively. Evaluation of ADMET pharmacokinetic properties and the drug likeness in silico revealed that only 3,5-dicaffeoylquinic acid, 3–4–5-tricaffeoylquinic acid, isorhamnetin-3-O-glucoside, and rubescensin A could be more effective drugs against COVID-19. Molecular dynamics (MD) simulations (100 ns) and MM-GBSA calculations confirmed the stability of ligand-protein complexes via hydrogen bonding interactions with crucial residues. The analysis of structural parameters (RMSD, RMSF, H-bonds, Rg, and SASA) indicates that 3,4,5-tricaffeoylquinic acid and rubescensin A compounds have good stability and significant binding affinity with the Mpro and S-RBD protein. Taken together, our findings confirm that Artemisia campestris as a plausible source of anti-SARS-COV-2 phytochemicals and suggest that may play important role in this activity.

Evaluation of the Role of Tanshinone I in an In Vitro System of Charcot-Marie-Tooth Disease Type 2N.

Charcot-Marie-Tooth disease type 2N (CMT2N) is an inherited nerve disorder caused by mutations in the alanyl-tRNA synthetase (AlaRS) gene, resulting in muscle weakness and sensory issues. Currently, there is no cure for CMT2N. Here, we found that all five AlaRS mutations in the aminoacylation domain can interact with neuropilin-1 (Nrp1), which is consistent with our previous findings. Interestingly, three of these mutations did not affect alanine activation activity. We then performed a high-throughput screen of 2000 small molecules targeting the prevalent R329H mutant. Using thermal stability assays (TSA), biolayer interferometry (BLI), ATP consumption, and proteolysis assays, we identified Tanshinone I as a compound that binds to and modifies the conformation of the R329H mutant and other CMT-related AlaRS mutants interacting with Nrp1. Molecular docking and dynamic simulation studies further clarified Tanshinone I's binding mode, indicating its potential against various AlaRS mutants. Furthermore, co-immunoprecipitation (Co-IP) and pull-down assays showed that Tanshinone I significantly reduces the binding of AlaRS mutants to Nrp1. Collectively, these findings suggest that Tanshinone I, by altering the conformation of mutant proteins, disrupts the pathological interaction between AlaRS CMT mutants and Nrp1, potentially restoring normal Nrp1 function. This makes Tanshinone I a promising therapeutic candidate for CMT2N.

Interactive Structural Analysis of KH3-4 Didomains of IGF2BPs with Preferred RNA Motif Having m6A Through Dynamics Simulation Studies.

m6A modification is the most common internal modification of messenger RNA in eukaryotes, and the disorder of m6A can trigger cancer progression. The GGACU is considered the most frequent consensus sequence of target transcripts which have a GGAC m6A core motif. Newly identified m6A 'readers' insulin-like growth factor 2 mRNA-binding proteins modulate gene expression by binding to the m6A binding sites of target mRNAs, thereby affecting various cancer-related processes. The dynamic impact of the methylation at m6A within the GGAC motif on human IGF2BPs has not been investigated at the structural level. In this study, through in silico analysis, we mapped IGF2BPs binding sites for the GGm6AC RNA core motif of target mRNAs. Subsequent molecular dynamics simulation analysis at 400 ns revealed that only the KH4 domain of IGF2BP1, containing the 503GKGG506 motif and its periphery residues, was involved in the interaction with the GGm6AC backbone. Meanwhile, the methyl group of m6A is accommodated by a shallow hydrophobic cradle formed by hydrophobic residues. Interestingly, in IGF2BP2 and IGF2BP3 complexes, the RNA was observed to shift from the KH4 domain to the KH3 domain in the simulation at 400 ns, indicating a distinct dynamic behavior. This suggests a conformational stabilization upon binding, likely essential for the functional interactions involving the KH3-4 domains. These findings highlight the potential of targeting IGF2BPs' interactions with m6A modifications for the development of novel oncological therapies.

Multifaceted exploration of acylthiourea compounds: In vitro cytotoxicity, DFT calculations, molecular docking and dynamics simulation studies

This study reports the synthesis and analysis of biologically active acylthiourea compounds (1 and 2) with a cyclohexyl moiety. The compounds were characterized using UV–Visible, FT-IR, 1H/13C NMR, and elemental analysis. The crystal structure of 2 was solved, revealing intra- and inter-molecular hydrogen bonds. Density functional theory (DFT) calculations provided insights into chemical reactivity and non-covalent interactions. Cytotoxicity assays showed the cyclohexyl group enhanced the activity of compound 2 compared to compound 1. Epoxide hydrolase 1 was predicted as the enzyme target for both compounds. We modeled the structure of epoxide hydrolase 1 and performed molecular dynamics simulation and docking studies. Additionally, in silico docking with SARS-CoV-2 main protease, human ACE2, and avian influenza H5N1 hemagglutinin indicated strong binding potential of the compounds. This integrated approach improves our understanding of the biological potential of acylthiourea derivatives.

Design and synthesis of new benzothiazole-piperazine derivatives and in vitro and in silico investigation of their anticancer activity

In this work, novel benzothiazole-piperazine acetamide (2a-2l) analogs were synthesized and evaluated their anticancer activity. The 1HNMR , 13CNMR and LC-MS/MS spectral data and elemental analyses were used to clarify the structure of the final molecules. The title compounds were procured by reacting 2‑chloro-N-(6-substituted benzothiazole-2-yl) acetamide with some piperazine derivatives. Cytotoxicity and apoptosis parameters including Annexin V binding capacities, effect on cell cycle, caspase-3 activation and mitochondrial membrane depolarization effect were evaluated to determine anticancer profile of the final molecules on A549 (human lung adenocarcinoma), C6 (glioma cell line) and NIH/3T3 (mouse embryoblast cell line). Mostly, the final molecules showed significant cytotoxic profile with prominent selectivity. 2c (IC50: 7.23±1.17, SI: 6.93), 2d (IC50: 17.50±4.95; SI: 11.59), and 2 h (IC50: 10.83±0.76; SI: 29.23) showed significant and selective cytotoxic activity. Compounds 2b, 2c and 2e provoked apoptosis of A549 cells with potential higher than cisplatin as determined by flow cytometry. The cell cycle analysis of 2b, 2e, 2 g, and 2 h suggested that the A549 cells were affected during G0/G1 phase. Caspase-3 activation was observed on cells by compounds 2a, 2e, 2i and 2l at most. The highest mitochondrial membrane depolarization ratios were seen treated by compounds 2e, 2 h, and 2j. None of the analogs displayed any obvious inhibition activity on MMP-9. The physicochemical properties were predicted for all compounds and also molecular docking and dynamics simulation studies were realized for compound 2e, namely N-(6-methoxybenzothiazol-2-yl)-2-(4-(p-tolyl) piperazin-1-yl) acetamide. The results indicated that merging benzothiazole and piperazine derivatives via acetamide bridge is promising in cancer research because these moieties can interact with the loop and ß-sheet regions of MMP-9. So, 2e was considered as a potential therapeutic agent against lung carcinoma.

Inhibition of monoamine oxidases and neuroprotective effects: chalcones vs. chromones.

Eighteen compounds derived from two sub-series, (HC1-HC9) and (HF1-HF9), were synthesized and evaluated for their inhibitory activities against monoamine oxidase (MAO). HC (chalcone) series showed higher inhibitory activity against MAO-B than against MAO-A, whereas the HF (chromone) series showed reversed inhibitory activity. Compound HC4 most potently inhibited MAO-B with an IC50 value of 0.040μM, followed by HC3 (IC50 = 0.049μM), while compound HF4 most potently inhibited MAO-A (IC50 = 0.046μM), followed by HF2 (IC50 = 0.075μM). The selectivity index (SI) values of HC4 and HF4 were 50.40 and 0.59, respectively. Structurally, HC4 (4-OC2H5 in B-ring) showed higher MAO-B inhibition than other derivatives, suggesting that the -OC2H5 substitution of the 4-position in the B-ring contributes to the increase of MAO-B inhibition, especially -OC2H5 (HC4) > -OCH3 (HC3) > -F (HC7) > -CH3 (HC2) > -Br (HC8) > -H (HC1) in order. In MAO-A inhibition, the substituent 4-OC2H5 in the B-ring of HF4 contributed to an increase in inhibitory activity, followed by -CH3 (HF2), -F (HF7), -Br (HF8), -OCH3 (HF3), and-H (HF1). In the enzyme kinetics and reversibility study, the Ki value of HC4 for MAO-B was 0.035 ± 0.005μM, and that of HF4 for MAO-A was 0.035 ± 0.005μM, and both were reversible competitive inhibitors. We confirmed that HC4 and HF4 significantly ameliorated rotenone-induced neurotoxicity, as evidenced by the reactive oxygen species and superoxide dismutase assays. This study also supports the significant effect of HC4 and HF4 on mitochondrial membrane potential in rotenone-induced toxicity. A lead molecule was used for molecular docking and dynamic simulation studies. These results show that HC4 is a potent selective MAO-B inhibitor and HF4 is a potent MAO-A inhibitor, suggesting that both compounds can be used as treatment agents for neurological disorders.

Structure-based design, synthesis, and biological characterization of indolylarylsulfone derivatives as novel human immunodeficiency virus type 1 inhibitors with potent antiviral activities and favorable drug-like profiles.

In the current antiretroviral landscape, continuous efforts are still needed to search for novel chemotypes of human immunodeficiency virus type 1(HIV-1) inhibitors with improved drug resistance profiles and favorable drug-like properties. Herein, we report the design, synthesis, biological characterization, and druggability evaluation of a class of non-nucleoside reverse transcriptase inhibitors. Guided by the available crystallographic information, a series of novel indolylarylsulfone derivatives were rationally discovered via the substituent decorating strategy to fully explore the chemical space of the entrance channel. Among them, compound 11h bearing the cyano-substituted benzyl moiety proved to be the most effective inhibitor against HIV-1 wild-type and mutant strains (EC50 = 0.0039-0.338 μM), being far more potent than or comparable to etravirine and doravirine. Besides, 11h did not exhibit cytotoxicity at the maximum test concentration. Meanwhile, the binding target of 11h was further confirmed to be reverse transcriptase (IC50 = 0.055 μM). Preliminary structure-activity relationship were discussed to guide further optimization work. Molecular docking and dynamics simulation studies were investigated in detail to rationalize the biological evaluation results. Further drug-likeness assessment indicated that 11h possessed excellent physicochemical properties. Moreover, no apparent hERG blockade liability and cytochrome P450 inhibition were observed for 11h. Notably, 11h was characterized by favorable in vitro metabolic stability with moderate clearance rates and long half-lives in human plasma and liver microsomes. Overall, 11h holds great promise as an ideal Anti-HIV-1 lead compound due to its potent antiviral efficacy, low toxicity, and favorable drug-like profiles.

Cimicifugoside H-2 as an Inhibitor of IKK1/Alpha: A Molecular Docking and Dynamic Simulation Study.

One of the most challenging issues scientists face is finding a suitable non-invasive treatment for cancer, as it is widespread around the world. The efficacy of phytochemicals that target oncogenic pathways appears to be quite promising and has gained attention over the past few years. We investigated the effect of docking phytochemicals isolated from the rhizomes of the Cimicifuga foetida plant on different domains of the IκB kinase alpha (IKK1/alpha) protein. The Cimicifugoside H-2 phytochemical registered a high docking score on the activation loop of IKK1/alpha amongst the other phytochemicals compared to the positive control. The interaction of the protein with Cimicifugoside H-2 was mostly stabilized by hydrogen bonds and hydrophobic interactions. A dynamic simulation was then performed with the Cimicifugoside H-2 phytochemical on the activation loop of IKK1/alpha, revealing that Cimicifugoside H-2 is a possible inhibitor of this protein. The pharmacokinetic properties of the drug were also examined to assess the safety of administering the drug. Therefore, in this in silico study, we discovered that the Cimicifugoside H-2 phytochemical inhibits the actively mutated conformation of IKK1/alpha, potentially suppressing the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway.

Targeting SARS-CoV-2 Spike and Main protease with phytochemicals from Herbs and spices: Molecular Docking and dynamics simulation studies.

Abstract COVID-19, a pandemic disease has affected 480 million people and caused 6 million deaths around the world. Despite the progress made in COVID-19 drug discovery, SARS-CoV-2, the causative agent of this disease continuously mutates and rapidly evolves into new variants. This increases the challenges in drug discovery for COVID-19. As natural products serve as sources of drugs forever, this study applies computational techniques in predicting the natural compounds in herbs and spices of household origin as SARS-CoV-2 spike and protease inhibitors and also verifies the top hits against spike and protease mutants associated with SARS-CoV-2 variants of concern. This study reveals Hesperidin, Diosgenin, Fenugreekine, Epigallocatechin gallate and Quercetin as SARS-CoV-2 spike and protease inhibitors, which acts better than the drug Remdesivir. The efficiency of the top hits was also been verified against the mutants, which reveals Diosgenin and Fenugreekine as the most efficient natural compounds against SARS-CoV-2 spike mutants (N501Y, E484K, K417N and K417T), which are associated with SARS-CoV-2 variants of concern. Additionally, Hesperidin is proven to have better binding efficiency against Mpro mutants (Y54C, A191V, T190I and N142S). Overall, this study concludes that Hesperidin, Diosgenin and Fenugreekine could combat both SARS-CoV-2 and its variants effectively.

Investigating emodin derivatives against SARS-CoV-2 found in medicinal herbs

SARS-CoV-2 continues to mutate and circulate at alarming levels around the world and is exemplified by the emergence of the new variant JN.1. The emergence of novel SARS-CoV variants underscores the urgency for the development of new drugs. Phytochemicals, known for their safety and efficacy, have been widely used to address various ailments. This study aims at identifying the anti-SARS-CoV potential of emodin, a bioactive anthraquinone, and its derivatives. Key proteins, including hemagglutinin-esterase (HE), papain-like protease (PLpro), major protease (3CLpro), non-structural protein (nsp3) and spike protein(S) of SARS-CoV, were used as protein targets for the virtual screening of 110 emodin derivatives (ED) and remdesivir a proven antiviral drug. Among the 110 derivatives, ED21, ED25, ED5 inhibited HE, 3CLpro and S protein, respectively. ED29 inhibited both PLpro and nsp3 with high binding affinity. Similar receptor binding sites were occupied by remdesivir and emodin derivatives. These emodin derivatives are bound to similar amino acids in receptors as compared to remdesivir. Further dynamic simulations studies with ED21-HE, ED25-3CLpro, ED5-S, ED29-PLpro and ED29-nsp3 complexes showed all of them are stable with minimum root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent-accessible surface area (SASA) and radius of gyration (Rg) and are comparable to APO protein. All the ligands accepted Lipinski's rule of five. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis revealed only ED21 and ED5 as promising druglike candidates that can have high therapeutic value and no side effects. These in-silico findings contribute to the development of potent SARS-CoV-2 inhibitors, potentially advancing the quest for effective antiviral drugs.

Novel Carbazoles as AChE Inhibitors: Synthesis, Molecular Docking and Dynamic Simulation Studies

Novel Carbazoles as AChE Inhibitors: Synthesis, Molecular Docking and Dynamic Simulation Studies

Synthesis, crystal structure, Hirshfeld, DFT, molecular docking, dynamics studies, and anti-cancer activity of 1-substituted-2-(4-(diethylamino)-2-hydroxyphenyl)- 1H-benzo[d]imidazole-5-ethyl carboxylates

In our present work, a novel series of 1-substituted-2–2-(4-(diethylamino)-2-hydroxyphenyl)- 1H-benzo[d]imidazole-5-ethyl carboxylates were synthesized by an efficient “one-pot” nitro reductive cyclization method using sodium dithionite is reported as potential anticancer agents. IR, 1H & 13C NMR and Mass spectral data confirmed the synthesized compounds' structure. Compound 6a and 6j were confirmed by their single crystal XRD studies. The Hirshfeld surfaces computational method was applied to visualize and analyse the intermolecular interactions within the crystal structure. All the synthesized compounds were assessed for in vitro anticancer activity towards human lung adenocarcinoma A549 cells and breast cancer MCF-7 cell lines. Compound 6j showed a promising activity with an IC50 value 42.7 μg/mL and 89.63 μg/mL against A549 and MCF-7 cell lines respectively. The potent compounds were assessed for cytotoxicity study on human embryonic kidney HEK 293 cell line and found to be non-toxic. Also, apoptosis study indicated compound 6j induced early apoptosis in the A549 lung adenocarcinoma and MCF-7 breast cancer cells. Molecular docking and dynamic simulation studies were carried out on human estrogen receptor protein (PDB: 3ERT).

Design of adaptive-PID-Smith control in the two-mixing tank series

ABSTRACT A control strategy must be developed to maintain the product composition of the two- or more-mixed-flow reactor series. In this research, a two-mixing tank series (TMTS) was utilized in the laboratory to approach the two-mixed flow reactors’ problems. Both tanks are designed to overflow so that the volume remains constant. The salt solution was directly fed to Tank 1, while the water was charged to both tanks as the mixing progressed. The output of Tank-1 flowed to Tank-2 through a rather long pipe, resulting in dead time in Tank-2. The Smith predictor was applied to overcome dead time. The PRC (process reaction curve) method was used to tune the PID (proportional-integral-derivative) parameters of Tank-1 and Tank-2. The novel composition controls, adaptive-PID (APID) and modified metaheuristic adaptive-PID (MMAPID), have been proposed and compared with conventional PID. The mathematical models were rigorously examined through XCOS simulations. The processing system is considered sensitive to changes in input disturbances since the process time constants of both tanks were quite low. The dead time of 0.5 minutes was found in Tank 2. The PID parameters produced by PRC experiments resulted in stable responses to changes in the disturbance system. As shown in the dynamic simulation study, both novel APID and MMAPID give almost the same results; their responses are faster than the conventional PID. Based on the integral absolute error (IAE) results, APID with scheduling PID parameters produced the smallest IAE and outperformed the conventional PID. The results of the study highlight APID and MMAPID potential in PID control applications for composition control in a TMTS. The combined APID-Smith and MMAPID-Smith were able to overcome the dead time well. This study creates opportunities for engineers and professionals to use cutting-edge control technologies, improving automation and chemical process industries.

2,3,5‐Trisubstituted Thiazolidinone Derivatives as Potential Antimicrobial and Antitubercular Agents and In Silico Studies

AbstractA series of novel 2,3,5‐trisubstituted thiazolidinone derivatives was designed and synthesized. Compounds were tested for their antimicrobial and antitubercular activities. Compounds 3‐(2,4‐difluorobenzyl)‐5‐[(5‐methylfuran‐2‐yl)methylidene]‐2‐(phenylimino)‐1,3‐thiazolidin‐4‐one (5 c) and 3‐(2,4‐difluorobenzyl)‐2‐((3‐fluorophenyl)imino)‐5‐((Z)‐4‐hydroxybenzylidene) thiazolidin‐4‐one (6 f) exhibited remarkable antimicrobial activity against Klebsiella pneumoniae and Escherichia coli respectively. All compounds except 3‐(2,4‐difluorobenzyl)‐5‐((3‐(4‐fluorophenyl)‐1‐phenyl‐1H‐pyrazol‐4‐yl)methylene)‐2‐(phenylimino)thiazolidin‐4‐one (5 a) and (6 f) exposed excellent antitubercular activity in comparison with the standard drugs against H37RV strain of Mycobacterium tuberculosis (ATCC No‐ 27294). In addition, molecular docking and dynamic simulations studies were performed with E. coli Mur B (EMB) (PDB ID: 2Q85), Aspergillus fumigatus sterol 14‐alpha demethylase (ASD) (PDB ID: 4UYM) and Mycobacterium tuberculosis pantothenate synthetase (MPS) (PDB ID: 3IVX) proteins against all compounds and the most potent compound (5 c) displayed higher binding proficiency. These compounds may serve as lead compounds for further optimization to achieve promising therapeutic properties.

Predictive insights into plant-based compounds as fibroblast growth factor receptor 1 inhibitors: a combined molecular docking and dynamics simulation study

The discovery of novel therapeutic agents with potent anticancer activity remains a critical challenge in drug development. Natural products, particularly bioactive phytoconstituents derived from plants, have emerged as promising sources for anticancer drug discovery. In this study, we used virtual screening techniques to explore the potential of bioactive phytoconstituents as inhibitors of fibroblast growth factor receptor 1 (FGFR1), a key signaling protein implicated in cancer progression. We used virtual screening techniques to analyze phytoconstituents extracted from the IMPPAT 2.0 database. Our primary objective was to discover promising inhibitors of FGFR1. To ensure the selection of promising candidates, we initially filtered the molecules based on their physicochemical properties. Subsequently, we performed binding affinity calculations, PAINS, ADMET, and PASS filters to identify nontoxic and highly effective hits. Through this screening process, one phytocompound, namely Mundulone, emerged as a potential lead. This compound demonstrated an appreciable affinity for FGFR1 and exhibited specific interactions with the ATP-binding site residues. To gain further insights into the conformational dynamics of Mundulone and the reference FGFR1 inhibitor, Lenvatinib, we conducted time-evolution analyses employing 200 ns molecular dynamics simulations (MDS) and essential dynamics. These analyses provided valuable information regarding the dynamic behavior and stability of the compounds in complexes with FGFR1. Overall, the findings indicate that Mundulone exhibits promising binding affinity, specific interactions, and favorable drug profiles, making it a promising lead candidate. Further experimental analysis will be necessary to confirm its effectiveness and safety profiles for therapeutic advancement in the cancer field. Communicated by Ramaswamy H. Sarma

Design, Synthesis and Evaluation of 8‐(Piperazin‐1‐yl) Imidazo[1,2‐a]Pyrazine Derivatives as Acetylcholinesterase Inhibitors and Antioxidants

AbstractA series of 8‐(piperazin‐1‐yl) imidazo [1,2‐a] pyrazine derivatives were designed and synthesized as acetylcholinesterase inhibitors (AChEIs) and antioxidants for the treatment of Alzheimer's disease (AD). Moreover, the biological evaluation results demonstrated that these synthesized compounds exhibited moderate inhibitory activities toward acetylcholinesterase (AChE) and radical scavenging activities. Among them, the compound with the strongest inhibitory activity against AChE had an IC50 value of 0.55 μM, which was higher than that of galantamine as the reference compound (IC50 value=5.01 μM). The compound with the strongest antioxidant activity had an IC50 value of 57.94 μM, which was lower than that of the ascorbic acid (IC50 value=25.70 μM) as the control drug. Furthermore, the results of molecular docking studies indicated that the compound could simultaneously bind to both catalytic active site (CAS) and peripheral anionic site (PAS) of AChE, which was consistent with the mixed inhibition pattern shown by enzyme kinetic studies. The interaction's stability was also assessed using a conventional atomistic 100 ns dynamics simulation study, which revealed the conformational stability of representative compound in the cavity of the AChE. In addition, the molecular properties of all compounds were predicted online through the SwissADME, and most compounds matched the properties of most orally administered drugs. Based on the biological activity and molecular properties, 8‐(piperazin‐1‐yl) imidazo[1,2‐a] pyrazine derivatives as AChEI were valuable for further development.

Impact of human walking on the pollutant removal effectiveness of direction air supply considering environmental disturbances: Dynamic simulation study

Direction air supply (DAS) is a computer vision-assisted ventilation mode designed to address the challenge of respiratory protection during human movement. The DAS parameter design is based on ideal, steady-state air distribution results, but it cannot reflect the dynamic protection performance. This work investigates the effect of human walking on the pollutant removal effectiveness of DAS through computational fluid dynamics simulation with the dynamic mesh method. This work formulates an occupant's movement pattern and implements walking and turning motions using the overset mesh method. To verify the feasibility of the dynamic simulation method, a walking experiment was conducted in an experimental chamber equipped with a DAS system. The evolution of concentration isosurfaces, as well as the concentration, velocity, and static pressure at breathing-zone height are revealed. The negative impacts of three common industrial environmental disturbances: localized high-temperature pollutants, ambient airflow, and distance between the DAS nozzle and the breathing zone, on the protective zone and the DAS barrier against pollutants are analyzed. To comprehensively evaluate the effectiveness of DAS, four assessment indexes are determined: inhalation exposure, protection factor, protective zone area, and effective protective ratio. The inconsistency between the protective zone area and the effective protective ratio needs to be noted. This work confirms the effectiveness of DAS within the protective zone and supports its further application in industrial settings.

1,3,5-triazine derivatives as potential anticancer agents against lung and breast cancer cell lines: Synthesis, biological evaluation, and structure-based drug design studies

Morpholine substituted 1,3,5-triazines have been recently recognized as potent inhibitors of PI3K-mTOR kinase signalling pathway. In this paper, we have performed synthesis and in vitro anti-cancer activity of trisubstituted 1,3,5-triazine derivatives against the A549 (Lung cancer) and MCF-7 (Breast cancer) cell lines. All synthesized analogs showed good inhibitory activity against both cell lines. Out of ten compounds, only two compounds, benzyl-4-(4-(4-(4-fluorophenyl)piperazin-1-yl)-6-morpholino-1,3,5-triazin-2-yl)piperazine-1-carboxylate (Compound 6b), shows 9.61 µM anticancer activity against A549 cell line and 22.68 µM activity against MCF-7 cell lines. Similarly, benzyl-4-(4-morpholino-6-thiomorpholino-1,3,5-triazin-2-yl)piperazine-1-carboxylate (Compound 6c) shows 39.70 µM anticancer activity against A549 cell line and 12.88 µM activity against MCF-7 cell lines. It shows that compound 6b is a potent inhibitor for A549 lung cancer cell line, and compound 6c shows excellent inhibitory activity for MCF-7 breast cancer cell line (9.16 µM and 12.88 µM, respectively). Both compounds (Compound 6b and Compound 6c) did not show toxicity to the non-cancerous HaCaT (Immortalized human keratinocytes) cells. Additionally, molecular descriptors of all synthesized compounds (6a-j) were calculated. After in vitro studies, the potent compounds 6b and 6c were validated using molecular docking and dynamics simulation studies and informed their binding affinities and conformational stability in the binding cavity. Structure-based drug design approach was followed for designing compounds based on potential ligand-receptor interaction. The result shows that triazine analogs serve as lead structures for generating new anti-cancer drugs.

Affinity Prediction of Shikonins Towards Sirtuins and the Requisite Structural Motifs for the Selective Inhibition of SIRT2 and SIRT3

Background: Shikonin and alkannin derivatives have various pharmacological activities with unknown mechanisms of action. Sirtuins are key intracellular enzymes involved in the cell cycle and metabolism and are ideal targets of therapeutic agents. Some evidence based on recent studies indicates that shikonins are possible modulators of sirtuins. Objective: In this study, an extensive computational workflow was utilized to assess the affinity of 27 different derivatives of shikonins towards SIRT1-6 as possible molecular targets. Methods: Molecular docking and dynamics simulation studies were performed, followed by MMPBSA analysis, and the results were compared with standard and selective sirtuin inhibitors. Subsequently, the scaffold hopping approach was used to find novel and more drug-like structures. Accordingly, the pharmacophoric features of 3,4-(Methylenedioxy)cinnamoyl alkannin in SIRT2 and SIRT3 were extracted and used for screening PubChem and Mcule databases. Results: The results indicated that 3,4-(Methylenedioxy)cinnamoyl alkannin is a potent SIRT2 and SIRT3 inhibitor and even more potent than the standard sirtuin inhibitors AGK2 and selisistat. The results successfully revealed some privileged fragments for the selective inhibition of SIRT2 and SIRT3. Conclusion: An indole or benzimidazole fragment linked to basic nitrogen through an amide would be an ideal structural feature for SIRT2 inhibition, and 3-methyl-2H-pyrazolo[3,4-b]pyridine was found to be a privileged fragment for optimal inhibition of SIRT3.