Docking Experiments Research Articles

HTLV-1 reverse transcriptase homology model provides structural basis for sensitivity to existing nucleoside/nucleotide reverse transcriptase inhibitors

The human T-lymphotropic virus type 1 (HTLV-1) infects millions of people globally and is endemic to various resource-limited regions. Infections persist for life and are associated with increased susceptibility to opportunistic infections and severe diseases including adult T cell leukemia/lymphoma and HTLV-1-associated myelopathy-tropical spastic paraparesis. No HTLV-1-specific anti-retrovirals have been developed and it is unclear whether existing anti-retrovirals developed for treatment of human immunodeficiency virus (HIV) have efficacy against HTLV-1. To understand the structural basis for therapeutic binding, homology modelling and machine learning were used to develop a structural model of the HTLV-1 reverse transcriptase. With this, molecular docking experiments using a panel of FDA-approved inhibitors of viral reverse transcriptases to assess their capacity for binding, and in turn, inhibition. Importantly, nucleoside/nucleotide reverse transcriptase inhibitor but not non-nucleoside reverse transcriptase inhibitors were predicted to bind the HTLV-1 reverse transcriptase, with similar affinity to HIV-1 reverse transcriptase. By strengthening the rationale for clinical testing of therapies such as tenofovir alafenamide, zidovudine, lamivudine, and azvudine for treatment of HTLV-1, this study has demonstrated the power of in silico structural biology approaches in drug design and therapeutic testing.

Mefentrifluconazole-Resistant Risk and Resistance-Related Point Mutation in FpCYP51B of Fusarium pseudograminearum.

Mefentrifluconazole, a triazole fungicide, exhibits remarkable efficacy in combating Fusarium spp. The mean EC50 value of mefentrifluconazole against 124 isolates of Fusarium pseudograminearum was determined to be 1.06 μg/mL in this study. Fungicide taming produced five mefentrifluconazole-resistant mutants with resistance factors ranging from 19.21 to 111.34. Compared to the original parental isolates, the fitness of three resistant mutants was much lower, while the remaining two mutants displayed enhanced survival fitness. There was evidence of positive cross-resistance between tebuconazole and mefentrifluconazole. Mefentrifluconazole resistance in F. pseudograminearum can be conferred by FpCYP51BL144F, which was identified in four mutants according to molecular docking and site-directed transformation experiments. Overexpression of FpCYP51s was also detected in the resistant mutants. In conclusion, mefentrifluconazole has a low-to-medium resistance risk in F. pseudograminearum, and the L144F mutation in FpCYP51B and the increased expression level of FpCYP51s may be responsible for mefentrifluconazole resistance in F. pseudograminearum.

A previously unidentified sugar transporter for engineering of high-yield Streptomyces.

Sugar transporters have significant contributions to regulate metabolic flux towards products and they are general potential targets for engineering of high-yield microbial cell factories. Streptomyces, well-known producers of natural product pharmaceuticals, contain an abundance of sugar transporters, while few of them are well characterized and applied. Here, we report a previously unidentified ATP-binding cassette (ABC) sugar transporter TP6568 found within a Streptomyces avermitilis transposon library, along with its key regulator GM006564. Subsequent in silico molecular docking and genetic experiments demonstrated that TP6568 possessed a broad substrate specificity. It could not only promote uptake of diverse monosaccharides and disaccharides, but also enhance the utilization of industrial carbon sources such as starch, sucrose, and dextrin. Constitutive overexpression of TP6568 resulted in decrease of residual total sugar by 36.16%, 39.04%, 38.40%, and 30.21% in engineered S. avermitilis S0, Streptomyces caniferus NEAU6, Streptomyces bingchenggensis BC-101-4, and Streptomyces roseosporus NRRL 11379 than their individual parent strain, respectively. Production of avermectin B1a, guvermectin, and milbemycin A3/A4 increased by 75.61%, 56.89%, and 41.13%, respectively. We then overexpressed TP6568 in combination with the regulator GM006564 in a high-yield strain S. avermitilis S45, and further fine-tuning of their overexpression levels boosted production of avermectin B1a by 50.97% to 7.02g/L in the engineering strain. Our work demonstrates that TP6568 as a promising sugar transporter may have broad applications in construction of high-yield Streptomyces microbial cell factories for desirable natural product pharmaceuticals. KEY POINTS: • TP6568 from Streptomyces avermitilis was identified as a sugar transporter • TP6568 enhanced utilization of diverse industrially used sugars in Streptomyces • TP6568 is a useful transporter to construct high-yield Streptomyces cell factories.

Synthesis, molecular docking, and antimicrobial activity of novel scaffolds based on bis(thiazole) linked to 2-phenoxy-N-arylacetamide as new hybrid molecules

The reaction of the appropriate bis(α-haloketones) with the corresponding thiosemicarbazones in EtOH at reflux in the presence of a few drops of TEA produced good yields of novel bis-thiazoles linked to 2-phenoxy-N-arylacetamide as novel hybrid molecules. The isomeric bis(thiazoles) were prepared under similar reaction conditions by reacting the appropriate bis(thiosemicarbazone) with the corresponding α-haloketones. All of the newly synthesized compounds were tested against four bacterial strains. Compounds 8g and 8i have the most antibacterial activity against S. aureus and Bacillus subtilis. The molecular docking studies supported our findings, which demonstrated that compounds 8g and 8i could fit with favorable binding energies in the active sites of bacterial DNA gyrase B and thymidylate kinase, respectively.

Muscone alleviates neuronal injury via increasing stress granules formation and reducing apoptosis in acute ischemic stroke

As the main bioactive component of musk, muscone has been reported to have marked protective effects in treating acute ischemic stroke (AIS). However, the specific anti-stroke mechanism of muscone still needs further research. In the current investigation, the PC12 cells OGD/R and the rat transient MCAO/R models were utilized as the AIS models. Serum hepatic and renal functional indexes (ALT, AST, BUN, and Cr) and cell viability were determined to select the appropriate muscone concentrations for in vitro and in vivo experiments. TTC, Hematoxylin and eosin (H&E), and Live/Dead staining were utilized to evaluate the protective effects of muscone in injured tissues and cells. Western blotting analysis, TUNEL staining, propidium iodide, and annexin V staining were applied to detect the anti-apoptotic effect of muscone. Double-label immunofluorescence staining of T-cell intracellular antigen-1 (TIA1) and Ras-GAP SH3 domain-binding protein 1 (G3BP1) was performed to observe whether muscone regulated the SG formation level. Molecular docking, TIA1 silencing and TIA1 overexpression experiments were employed to investigate the molecular mechanism underlying the regulation of SG formation by muscone. The 2, 3, 5-Triphenyl-tetrazolium chloride (TTC) staining and live/dead staining showed the AIS injury level of MCAO/R rat and the OGD/R PC12 cells were attenuated by muscone administration. The muscone significantly minimized the apoptosis rate in MCAO/R rats and OGD/R PC12 cells following flow cytometry analysis, western blotting analysis, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. The double-label immunofluorescence staining data revealed that muscone promoted the SG formation level in OGD/R PC12 cells and the cortex MCAO/R rats. The results of molecular docking, TIA1 silencing and TIA1 overexpression experiments revealed that muscone could bind to TIA1 protein and regulate its expression level, thereby promoting the formation of stress granules and exerting a protective effect against AIS injury. This study indicated that the significant protective effect of muscone in reducing apoptosis levels might be via promoting SG formation under AIS conditions. This study further explores the therapeutic effect and anti-apoptosis mechanism of muscone in AIS, which may provide a potential candidate drug for the clinical treatment of AIS injury.

New perspectives on the potential of tetrandrine in the treatment of non-small cell lung cancer: bioinformatics, Mendelian randomization study and experimental investigation.

Although there are numerous treatment methods for NSCLC, long-term survival remains a challenge for patients. The objective of this study is to investigate the role and causal relationship between the target of tetrandrine and non-small cell lung cancer (NSCLC) through transcriptome and single-cell sequencing data, summary-data-based Mendelian Randomization (SMR) and basic experiments. The aim is to provide a new perspective for the treatment of NSCLC. We obtained the drug target gene of tetrandrine through the drug database, and then used the GSE19188 data set to obtain the NSCLC pathogenic gene, established a drug-disease gene interaction network, screened out the hub drug-disease gene, and performed bioinformatics and tumor cell immune infiltration analysis. Single-cell sequencing data (GSE148071) to determine gene location, SMR to clarify causality and drug experiment verification. 10 drug-disease genes were obtained from 213 drug targets and 529 disease genes. DO/GO/KEGG analysis showed that the above genes were all related to the progression and invasion of NSCLC. Four drug-disease genes were identified from a drug-disease PPI network. These four genes were highly expressed in tumors and positively correlated with plasma cells, T cells, and macrophages. Subsequent single-cell sequencing data confirmed that these four genes were distributed in epithelial cells, and SMR analysis revealed the causal relationship between CCNA2 and CCNB1 and the development of NSCLC. The final molecular docking and drug experiments showed that CCNA2 and CCNB1 are key targets for tetrandrine in the treatment of NSCLC.

Synthesis, Antioxidant and Antituberculosis Evaluation of Eugenol Derivatives from Mannich Condensation

AbstractMannich bases are interesting class of molecules thanks to their various pharmacological properties. This paper presents the synthesis and characterization of eugenol derivatives following Mannich condensation. The in vitro antituberculosis activity of the synthesized derivatives was evaluated by the Resazurin microtiter assay (REMA). The 2,2′‐diphenyl‐1‐picrylhydrazyl (DPPH) free radical scavenging and ferrous cation (FeCl2) chelating tests were used to estimate the antioxidant capacity. All eugenol Mannich bases inhibited the Mycobacterium tuberculosis (Mtb) H37Rv growing. Those of 2‐dimethylaminomethyl‐6‐methoxy‐4‐propenylphenol (1) and 2‐methoxy‐4‐propenyl‐6‐pyrrolidinylmethylphenol (4) were the most active at 10 μg/mL. Additionally, significant antioxidant profile was exhibited by the synthesized derivatives, especially for 2‐dicyclohexylaminomethyl‐6‐methoxy‐4‐propenylphenol (5) that showed an antiradical activity of EC50=20 μg/mL, twice as strong as that of eugenol precursor, and for 2‐methoxy‐6‐methylpiperazinylmethyl‐4‐propenylphenol (3) and compound 4, which were promising iron chelators with EC50 of 0.016 and 0.018 mg/mL, respectively, better than EDTA standard. The molecular docking experiments on two different antituberculosis receptors showed excellent binding affinity of compounds 4 and 5 into the active site of pantothenate kinase (PanK, type I), suggesting PanK as potential molecular target. These encouraging findings showed the importance of Mannich reaction for the development of antitubercular candidates and the improvement of natural products bioactivity.

Secondary metabolites from the leaves of Terminalia myriocarpa and their α-glucosidase inhibitory potential

The objective of this study is to investigate the chemical composition of the leaves of Terminalia myriocarpa and to evaluate their α-glucosidase inhibitory activity aiming to be used as a safe antidiabetic. Consequently, 10 compounds were isolated using column and preparative thin-layer chromatographic techniques and identified as alphitolic acid, isovitexin, flavogallonic acid, nigaichigoside F1, quercetin, quadranoside IV, rosamultin, 19α-hydroxyasiatic acid, asiatic acid, and arjunic acid. Structure elucidation was based on chemical (acid hydrolysis) and spectroscopic (UV, 1 H, and 13C-NMR) analyses and findings were confirmed through comparison with published data. The α-glucosidase inhibitory activity of the methanol extract fractions and compounds isolated therefrom was evaluated in-vitro alongside that of acarbose (positive control). Results revealed that quercetin and flavogallonic acid were significantly active with half-maximal inhibitory concentrations (IC50) equal to 7.5 ± 0.09 and 21.0 ± 1.4 µM, respectively. Furthermore, the interaction of lavogallonic acid with α-glucosidase enzyme was verified by docking experiment. Accordingly, quercetin and flavogallonic acid could be considered safer natural alternatives to the currently availableα-glucosidase inhibitors.

Molecular docking and in vitro biological studies of a Schiff base ligand as anticancer and antibacterial agents

In this study, a bis-Schiff base ligand of N,N'-bis(4-dimethylaminobenzylidene)hexane-1,6-diamine (L) was obtained via a condensation reaction of N, N-dimethylaminobenzaldehyde and hexane-1,6-diamine. The ligand (L) was characterized by various analysis tools such as FT-IR, 1H and 13C NMR, Mass, DRS spectra, XRD, and thermal analyses. The ligand (L) inhibitory action was also assessed against two gram-negative and four gram-positive bacterial pathogens. Disk diffusion, MIC, and MBC test results indicate that the investigated ligand (L) has antibacterial activity against bacteria and can be employed as a therapeutic candidate after further research. The MTT assay was used to study the ligand (L) cytotoxicity on the MCF-7 cell line and calculate the IC50. Cell treatment with ligand (L) in various concentrations showed that the bis Schiff base ligand (IC50 = 6.27 ± 0.07 mgmL−1) is the most significant. Assessment of in silico ADMET ligand (L) properties illustrates that showed agreement with Lipinski’s rule of five. Lastly, the interaction between the ligand with 1STE, 1Z11, and 1AJ6 receptors was examined using docking experiments. The best conformation with the lowest affinity energy (−6.57 kcalmol−1) corresponds to the interaction of the ligand (L) with the active site of the 1Z11 receptor.

Synthesis, crystal structure, spectroscopic characterization, in vitro and in silico studies of water-soluble (Z)-N'-hydroxy-2-morpholinonicotinimidamide

A water-soluble compound (Z)-N'-hydroxy-2-morpholinonicotinimidamide was synthesized, and it has a multi-functional group, such as morpholine, pyridine, and oxime. The synthesized compound was characterized by various spectroscopic techniques such as NMR, FT-IR, UV-visible, Elemental analysis, and single-crystal XRD. The molecule was investigated using computational methods, such as DFT and MEP, to determine the electronic characterization of the molecule's surface. With the aid of these studies, docking experiments were also performed with diabetic and inflammatory-responsible enzymes. The results are matched with in vitro anti-diabetic and anti-inflammatory studies where protein inhibition methods were followed. The acquired results strongly imply that the compound may be investigated for better activity in vivo studies, given that it can support the biological system regarding solubility.

AGXT2 Suppresses the Proliferation and Dissemination of Hepatocellular Carcinoma Cells by Modulating Intracellular Lipid Metabolism.

Alanine glyoxylate aminotransferase (AGXT) family members are crucial in cancer processes, but their role in hepatocellular carcinoma (HCC) metabolism is unclear. This study investigates AGXT2's function in HCC. AGTX2 expression was studied using bioinformatics, real-time reverse transcriptase-polymerase chain reaction (RT-qPCR), Western blot, and Enzyme-linked immunosorbent assay (ELISA). A lentivirus-induced AGTX2 overexpression cell model was analyzed with RNA sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS). Cholesterol levels were confirmed by Oil Red O staining. AGTX2 effects were evaluated through cell cycle analysis, wound healing, and transwell migration assays.Tumorigenic effects were observed in NOD-SCID IL2Rγnull (NTG) mice in subcutaneous experiments. Protein interaction was examined through co-immunoprecipitation methods. We observed a significant reduction in AGXT2 mRNA and protein levels in both HCC tumor tissues and serum samples from patients with liver cancer, which was associated with a worse prognosis. The activation of AGXT2 has been shown to effectively decrease cholesterol levels in liver cancer cells, serving as an antagonist in the cholesterol metabolism pathway. An increase in low density lipoprotein receptor (LDLR) mRNA was noted in cells overexpressing AGXT2, accompanied by a decrease in LDLR protein and an elevation in proprotein convertase subtilisin/kexin type 9 (PCSK9) mRNA and protein levels. Molecular docking and co-immunoprecipitation experiments further elucidated the interaction between AGXT2 and LDLR proteins. AGXT2 was observed to suppress the migratory and invasive capabilities of HCC cells, inducing cell cycle arrest in the G2/M phase. AGXT2 activation inhibited subcutaneous liver cancer tumor growth in NTG mice. AGXT2 was found to lower cholesterol levels in liver cancer cells, possibly through interactions with the LDLR protein and modulation of PCSK9-mediated LDLR degradation. This mechanism may impede cholesterol transport to liver cancer cells, thereby suppressing their growth and metastasis.

Activity of fungicide cyclobutrifluram against Fusarium fujikuroi and mechanism of the pathogen resistance associated with point mutations in FfSdhB, FfSdhC2 and FfSdhD

Rice bakanae disease (RBD) is a devastating plant disease caused by Fusarium fujikuroi. This study aimed to evaluate the potential of cyclobutrifluram, a novel succinate dehydrogenase inhibitor (SDHI), to control RBD, and determine the risk and mechanism of resistance to cyclobutrifluram in F. fujikuroi. In vitro experiments showed that cyclobutrifluram significantly inhibited mycelial growth and spore germination, and altered the morphology of mycelia and conidia. Treatment with cyclobutrifluram significantly decreased mycotoxin production and increased cell membrane permeability in F. fujikuroi. The baseline sensitivity of 72 F. fujikuroi isolates to cyclobutrifluram was determined using mycelial growth and spore germination inhibition assays, which revealed EC50 values of 0.0114 – 0.1304 μg mL-1 and 0.0012 – 0.016 μg mL-1, with mean EC50 values of 0.0410 ± 0.0470 μg mL-1 and 0.0038 ± 0.0015 μg mL-1, respectively. Pot experiments demonstrated that the protective effect of cyclobutrifluram against F. fujikuroi was more significant than that of phenamacril and azoxystrobin, indicating that cyclobutrifluram is a promising antifungal agent for the control of RBD. Six cyclobutrifluram-resistant mutants of F. fujikuroi were obtained via fungicide adaptation. Moreover, these mutants exhibited weaker fitness than their parental isolate and positive cross-resistance with other SDHI fungicides, including pydiflumetofen and penflufen; however, no cross-resistance was detected with other classes of fungicides, including phenamacril, fludioxonil, prochloraz, or azoxystrobin. These results indicated that the resistance risk of F. fujikuroi to cyclobutrifluram might be moderate. Sequencing analysis revealed that mutations, including H248D in FfSdhB, A83V in FfSdhC2, and S106F and E166K in FfSdhD, contributed to resistance, which was confirmed by molecular docking and homologous replacement experiments. The results suggest a high potential for cyclobutrifluram to control RBD and a moderate resistance risk of F. fujikuroi to cyclobutrifluram, which are meaningful findings for the scientific application of cyclobutrifluram.

Exploration of Dan-Shen-Yin against pancreatic cancer based on network pharmacology combined with molecular docking and experimental validation

Traditional Chinese Medicine (TCM) introduces a potentially effective strategy in the realm of cancer therapy, whereas network pharmacology provides a reliable mechanism for clarifying the complex interplay between active constituents and their corresponding targets. Although Dan-Shen-Yin (DSY) has demonstrated remarkable efficacy in the treatment of various diseases, its potential anti-pancreatic cancer effects and underlying mechanisms remain unexplored. The present study aims to validate the anti-pancreatic cancer efficacy of DSY both in vivo and in vitro, while also elucidating its mechanism through a combination of network pharmacology, molecular docking, and related experiments. The in vivo effectiveness of DSY was validated using the patient-derived xenograft (PDX) model, which was chosen due to its remarkable capacity to maintain the essential histological and genetic attributes of the primary tumor. Network pharmacology predicted the anti-pancreatic cancer efficacy of DSY, which was confirmed by in vitro experiments showing inhibitory effects on proliferation, pro-apoptosis, migration, and colony formation of PC cells. Molecular docking studies further confirmed that the active components of DSY exhibited good nucleophilicity for the selected target proteins through their ability to interact via hydrogen bonding and Van der Waals forces. The PDX model showed that DSY effectively inhibited tumor growth and improved prognosis. Experiments conducted both in vivo and in vitro have demonstrated that DSY is an effective treatment for PC. Moreover, mechanistic investigations have provided evidence of the ability to impede the EGFR/SRC/STAT3 signaling pathway.

Exploring the effect and mechanisms of Epimedium on diabetic testicular injury using network pharmacology, molecular docking, and cell experiments

Exploring the effect and mechanisms of Epimedium on diabetic testicular injury using network pharmacology, molecular docking, and cell experiments

Roburic acid inhibits lung cancer metastasis and triggers autophagy as verified by network pharmacology, molecular docking techniques and experiments.

Roburic acid (ROB) is a newly discovered tetracyclic triterpene acid extracted from oak galls, which has anti-inflammatory effects, but the mechanism of its anticancer effect is not clear. Our study focuses on exploring the potential mechanism of action of ROB in the treatment of lung cancer using a combination of network pharmacological prediction, molecular docking technique and experimental validation. A network pharmacology approach was used to screen the protein targets of ROB and lung cancer, and PPI network analysis and enrichment analysis were performed on the intersecting genes. The tissue and organ distribution of the targets was also evaluated based on the BioGPS database. To ensure the reliability of the network pharmacology prediction results, we proceeded to use molecular docking technique to determine the relationship between drugs and targets. Finally, in vitro experiments with cell lines were performed to further reveal the potential mechanism of ROB for the treatment of lung cancer. A total of 83 potential targets of ROB in lung cancer were collected and further screened by using Cytoscape software, and 7 targets of PTGS2, CYP19A1, PTGS1, AR, CYP17A1, PTGES and SRD5A1 were obtained as hub genes and 7 hub targets had good binding energy with ROB. GO and KEGG analysis showed that ROB treatment of lung cancer mainly involves Arachidonic acid metabolism, Notch signaling pathway, cancer pathway and PPAR signaling pathway. The results of in vitro experiments indicated that ROB may inhibit the proliferation and metastasis of lung cancer cells and activate the PPARγ signaling pathway, as well as induce cellular autophagy. The results of this study comprehensively elucidated the potential targets and molecular mechanisms of ROB for the treatment of lung cancer, providing new ideas for further lung cancer therapy.

Exploring the most promising anti - Depressant drug targeting Microtubule Affinity Receptor Kinase 4 involved in Alzheimer's Disease through molecular docking and molecular dynamics simulation.

Alzheimer's Disease (AD) is the prevailing type of neurodegenerative illness, characterised by the accumulation of amyloid beta plaques. The symptoms associated with AD are memory loss, emotional variability, and a decline in cognitive functioning. To date, the pharmaceuticals currently accessible in the marketplace are limited to symptom management. According to several research, antidepressants have demonstrated potential efficacy in the management of AD. In this particular investigation, a total of 24 anti-depressant medications were selected as ligands, while the Microtubule Affinity Receptor Kinase 4 (MARK4) protein was chosen as the focal point of our study. The selection of MARK4 was based on its known involvement in the advancement of AD and other types of malignancies, rendering it a highly prospective target for therapeutic interventions. The initial step involved doing ADMET analysis, which was subsequently followed by molecular docking of 24 drugs. This was succeeded by molecular dynamics simulation and molecular mechanics generalised Born surface area (MMGBSA) calculations. Upon conducting molecular docking experiments, it has been determined that the binding affinities observed fall within the range of -5.5 kcal/mol to -9.0 kcal/mol. In this study, we selected six anti-depressant compounds (CID ID - 4184, 2771, 4205, 5533, 4543, and 2160) based on their binding affinities, which were determined to be -9.0, -8.7, -8.4, -8.3, -8.2, and -8.2, respectively. Molecular dynamics simulations were conducted for all six drugs, with donepezil serving as the control drug. Various analyses were performed, including basic analysis and post-trajectory analysis such as free energy landscape (FEL), polarizable continuum model (PCM), and MMGBSA calculations. Based on the findings from molecular dynamics simulations and the MMGBSA analysis, it can be inferred that citalopram and mirtazapine exhibit considerable potential as anti-depressant agents. Consequently, these compounds warrant further investigation through in vitro and in vivo investigations in the context of treating AD.

Design, synthesis, and biological evaluation of novel thiazole derivatives as PI3K/mTOR dual inhibitors.

The development of anticancer drugs targeting both PI3K and mTOR pathways is recognized as a promising cancer therapeutic approach. In the current study, we designed and synthesized seventeen new thiazole compounds to investigate their effect on both PI3K and mTOR as well as their anti-apoptotic activity. All the synthesized thiazoles were investigated for their antiproliferative activity on a panel of 60 different cancer cell lines at the National Cancer Institute. Compounds 3b and 3e were selected for further investigation at five dose concentrations due to their effective growth inhibiting activity. Compounds 3b and 3e were further evaluated for their in vitro inhibitory activities against PI3Kα and mTOR compared to alpelisib and dactolisib, respectively as reference drugs. The inhibitory effect of compound 3b on PI3Kα was similar to alpelisib, but it showed weaker inhibitory activity on mTOR compared to dactolisib. Moreover, compound 3b exhibited significantly higher inhibitory activity compared to compound 3e against both PI3Kα and mTOR. The cell cycle analysis showed that compounds 3b and 3e induced G0-G1 phase cell cycle arrest in the leukemia HL-60(TB) cell line. Meanwhile, they significantly increased the total apoptotic activity which was supported by an increase in the level of caspase-3 in leukemia HL-60(TB) cell lines. Molecular docking experiments provided additional explanation for these results by demonstrating the ability of these derivatives to form a network of key interactions, known to be essential for PI3Kα/mTOR inhibitors. All these experimental results suggested that 3b and 3e are potential PI3Kα/mTOR dual inhibitors and could be considered promising lead compounds for the development of anticancer agents.

The discovery of novel imidazo[1,2-a]pyridine derivatives as covalent anticancer agents.

The success of targeted covalent inhibitors (TCIs) for treating cancers has spurred the search for novel scaffolds to install covalent warheads. In our endeavour, using a scaffold hopping strategy, we managed to utilize imidazo[1,2-a]pyridine as the core backbone and explored its potential for the development of covalent inhibitors, therefore, synthesizing a series of novel KRAS G12C inhibitors facilitated by the Groebke-Blackburn-Bienaymè reaction (GBB reaction). Preliminary bio-evaluation screening delivered compound I-11 as a potent anticancer agent for KRAS G12C-mutated NCI-H358 cells, whose effects were further clarified by a series of cellular, biochemical, and molecular docking experiments. These results not only indicate the potential of compound I-11 as a lead compound for the treatment of intractable cancers, but also validate the unique role of imidazo[1,2-a]pyridine as a novel scaffold suitable for the discovery of covalent anticancer agents.

Cinnamate-amine hybrids: Antituberculosis activity and molecular docking

Antituberculosis activity and molecular docking experiments were performed on 14 cinnamate-amine hybrids. Cinnamamides 1a,b,c,d,i,j effectively inhibited the growth of Mycobacterium tuberculosis H37Rv, with cinnamamide 1c having the highest inhibition effects with a minimum inhibitory concentration value of 3.13 μg/ml. Based on the docking results, the molecule of cinnamamide 1c (binding energy of −4.13 kcal/mol) was found to be stretched from the edge of the active site to its sub-binding pocket, referred to as an extended conformation when binding to the InhA active site. Cinnamamide 1c turned out to be an inhibitor whose potency is unaffected by the conserved interaction network with the catalytic residue Tyr158. These findings suggest these cinnamate-amine hybrids as potential lead compounds in developing new antituberculosis drugs.

Understanding selective sensing of human serum albumin using a D-π-A probe: a photophysical and computational approach.

The human serum albumin (HSA) level is a valuable indicator of an individual's health status. Therefore, its detection/estimation can be used to diagnose several diseases. In this work, we have developed a series of donor-π-acceptor probes, which were found to selectively detect HSA over BSA (bovine serum albumin). Among these probes, A4, which bears the trifluoroacetyl group, showed the highest selectivity for HSA, with limits of detection and quantification being 1.36 nM and 2.59 nM, respectively. CD spectroscopy of the HSA-A4 ensemble indicated an increase in the α-helicity of the protein, while the displacement assays revealed the localization of the probe in the hemin site of HSA. The probe works on the principle of excited state intramolecular charge transfer (ICT). Its selectivity was also validated computationally. Docking experiments confirmed the preference of the probe for the hemin binding IB site of HSA, as observed from the fluorescence displacement assay results, and a comparison of docking scores demonstrated the greater preference of A4 for HSA compared to BSA. Computational experiments also showed a change in preference for HSA amino acid residues exhibited by the excited state of probe A4 (Tyr161, Met123, Pro118, and Leu115) when compared to its ground state (Arg186 and His146). Hydrophobic interactions dominated the excited state protein-probe ensemble, whereas there was significant involvement of the water bridges along with the hydrophobic interactions in the ground state ensemble. Probe A4 was also assessed for its practical utility and found to successfully sense HSA in urine at extremely low concentrations. Moreover, the A4-HSA ensemble was employed for hemin sensing with a detection limit of 0.23 μM.