Active Site Of Receptor Research Articles

Design, synthesis, and biological investigations of new pyrazole derivatives as VEGFR2/CDK-2 inhibitors targeting liver cancer

New Series of N-Manniche bases 3,4 (a-c) and 5,6 (a-b) were synthesized through the reaction of benzaldehyde and amine with 3-methyl-4-(aryldiazenyl)-1H-pyrazol-5-ol derivatives 2(a-c), they were fully characterized by FT-IR, (1H, 13C) NMR data in addition to their mass spectra. The Structural Activity Relationship of the target compounds were examined for their cytotoxicity. Some newly synthesized compounds showed promising antiproliferation properties when tested against HepG2 cancer cells. Compounds 4a, 5a, and 6b showed potent cytotoxicity against HepG2 with IC50 values of 4.4, 3.46 and 2.52 µM compared to Sorafenib (IC50 = 2.051 µM) and Roscovitine (IC50 = 4.18 µM). Furthermore, they were safe against the THLE2 cells with higher IC50 values. Compound 6b exhibited promising dual VEGFR2/CDK-2 inhibition activities; it had an IC50 value of 0.2 μM with VEGFR2 inhibition of 93.2%, and it had an IC50 value of 0.458 μM with CDK-2 inhibition of 88.7%. In comparison to the untreated control group (0.95%), compounds 5a (38.32%) and 6b (42.9%) considerably increased the cell population in total apoptosis. In addition, compounds 5a and 6b arrested the cell population at G0-G1 and S phases, respectively. Molecular docking experiments confirmed the virtual binding mechanism of the most active drugs, which were found to have good binding affinities with both receptor active sites.

In silico screening and identifying phytoconstituents of Withania somnifera as potent inhibitors of BRCA1 mutants: A therapeutic against breast cancer

Breast CAncer gene 1 (BRCA1) is an anti-oncogene that helps the cell repair damaged DNA and preserve genetic material. BRCA1 also acts as a cell growth suppressor and produces tumor suppressor gene (TSG) proteins, i.e., BRCA1 protein. Remarkably, BRCA1 mutations account for 90 % of hereditary breast cancer and a majority of hereditary ovarian cancer. Hence, we have considered three mutants of BRCA1 (R1699W, R1699Q, T1700A) in this study and adopted an in-silico approach to find the best possible phytochemical to inhibit these mutated proteins, enabling early breast cancer diagnosis. Perceiving the importance, many natural molecules from ancient medicinal plants are considered for molecular docking. Our findings suggest that though many molecules bind actively with the receptor's active site, the top three phytoconstituents (27-Deoxy-14-hydroxywithaferin A, Withacoagulin, Somniferanolide) of Withania somnifera, commonly known as Ashwagandha, have high binding affinities and suitable pharmacokinetic properties, making these natural compounds potential drug candidates. Further, molecular dynamics (MD) simulation and the binding free energy calculation show stability and thermodynamically favourable. We can, therefore, draw the conclusion that these lead compounds act as potential inhibitors against BRCA1. However, wet lab experiments and clinical trials are recommended to ascertain its efficacy, hence the development of novel BRCA1 inhibitors.

Synthesis, Crystal Structure, DFT Calculations, Bioactivity Study, and Docking Results of Bis‐Hydrazone Based on 1,2,4‐Triazol‐3‐Thione

AbstractThe new, unexpected bioactive bis‐hydrazone derivative (4) was obtained, in 74 % yield, by reacting two molar equivalents of pyrazole‐4‐carbaldehyde (1) with one molar equivalent of 2,5‐dihydrazineyl‐1,3,4‐thiadiazole (2). The compound was comprehensively characterized, including X‐ray single crystal, DFT calculations, and bioactivity assessments. Hirschfeld surface analysis confirmed the presence of hydrogen bonding interactions, particularly N−H⋅⋅⋅N and C−H⋅⋅⋅π interactions, which influence the overall crystal packing. The target bis‐hydrazone exhibited significant antimicrobial activity against multi‐drug‐resistant bacterial strains, with the largest activity against S.typhimurium with an inhibition zone of 17.1±0.6 mm and MIC 31.25 μg/mL. The compound also demonstrated significant cytotoxic effects on cancer cells, with a higher IC50 ratio of 134.43 μg/mL against the normal cell line Wi38 and the lowest IC50 value of 45.88 μg/mL against the cancer cell line Caco2. Molecular docking was carried out with estrogen receptor alpha (ERα) and sodium‐glucose transporter SGLT1, which are relevant to Mcf7 and Caco2 cancer cell lines, respectively. Docking suggests the presence of specific amino acids that may influence the binding affinity between the ligand and receptor active sites through residue overlaps in chains A for SGLT1 and B for Erα, offering the ligand as a promising anticancer consistent with the IC50 outcomes.

Homology Modelling and Molecular Docking Studies to Discover Potent Inhibitors of CD169 in PRRSV Infection

CD169 is one of the putative receptors of porcine reproductive and respiratory syndrome virus, also plays a major role in PRRSV infection. Computational methods including, homology modelling, molecular docking analysis and molecular dynamics simulations carried out to investigate 3D structure and potent inhibitors of CD16. Homology modelling and molecular docking were done by Maestro 10.6. A 3D structure of CD169 was obtained through homology modelling. It was later subjected protein-ligand interaction by molecular docking study. The docking results showed top ten hits compounds with the docking score energies, among those compounds MOL002433 (3R,8S,9R,10R,13R,14S,17R)-3-hydroxy-4,4,9,13,14-pentamethyl-17-[(E,2R)-6-methyl-7-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxyhept-5-en-2-yl]-1,2,3,7,8,10,12,15,16,17-decahydr) had the best docking score energy -8.095 kcal/mol and showed significant binding affinity and interactions with CD169 receptor active site, respectively form H bond with residues ASP-40, SER-104, LYS-107 and ASN-92. Furthermore, MD (molecular dynamics) simulations were performed by Amber 16 to investigate the stability of a ligand-protein complex. The analysis of root mean square deviation (RMSD) of CD169 /(3R,8S,9R,10R,13R,14S,17R)-3-hydroxy-4,4,9,13,14-pentamethyl-17-[(E,2R)-6-methyl-7-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxyhept-5-en-2-yl]-1,2,3,7,8,10,12,15,16,17-decahydr) complex revealed that CD169 protein has more stability when it interacts with the inhibitor. These findings have given us a better understanding of the functional properties and the reaction mechanism of CD169 receptor. Our results will help to identify new leads for drug discovery in PRRSV infection.

Interfacial adsorption and catalysis of single-atom Pt-loaded ZrO2 surfaces for enhancing formaldehyde oxidation

The emerging transition metal single-atom catalysts (SACs) are expected to have high activity for converting detrimental formaldehyde (HCHO) under mild conditions. Currently, the exploitation of novel SACs with designed or modified support surfaces remains largely imperative. Herein, we used density functional theory to explore the catalytic performance for HCHO oxidation on various single-atom Pt-loaded ZrO2 surfaces, in which oxygen vacancy and lattice hydroxyl group were included on the surfaces. The surface modifications could enhance the co-adsorption of HCHO and O2 molecules and provide more active sites due to interfacial electron redistribution. The transition state search approach was applied to investigate the oxidation pathways on various ZrO2-supported SAC surfaces, wherein distinct dehydrogenation mechanisms and intermediates were clarified. The oxygen vacancy defects and hydroxyl groups can enhance the catalytic activity for HCHO oxidation by providing active receptor sites for the H-transfer and facilitating the CH bond breakage. Microkinetic modeling was further used to characterize the reaction rates and kinetics behavior of HCHO oxidation on the SAC surfaces. Our simulation demonstrates the excellent catalytic performance of the modified ZrO2-supported SAC in the HCHO oxidation. Meanwhile, the mechanism is also an important implication for the synthesis and design of novel SACs.

In-silico molecular docking, ADME study, and molecular dynamic simulation of new azetidin-2-one derivatives with antiproliferative activity

Over the past two decades, protein kinase has been a heavily studied target in the development of new anti-proliferative medications. Heterocyclic systems have been identified as the preferred scaffold because of their wide range of biological properties. In this research, the objective was to design and develop fifteen novel azetidin-2-one derivatives and assess their cytotoxic potential as inhibitors of the epidermal growth factor receptor, which is considered one of the key factors influencing cell growth and proliferation. The crystal structure of inactive EGFR tyrosine kinase domain ligand erlotinib from protein data bank was retrieved in order to be docked with our proposed azetidine-2-one derivatives to evaluate their activity as anti-proliferative agents. In this article, an in-silico molecular docking approach proposes that these azetidine-2-one derivatives have satisfactory binding contact with the erlotinib binding site. Although, three compounds have been identified as the most powerful as they have PLP fitness scores of (77.79, 76.68 and 71.46), respectively, while the reference ligand’s fitness score was (71.94). Additionally, all of our derivatives have satisfied the Swiss-ADME parameters, indicating that they may be orally active compounds. In conclusion, two compounds (A-2 and A-8) have better PLP fitness, and one (A-14) has a comparable score in comparison to the reference ligand, at the active site of epidermal growth factor receptor. indicating that the novel azetidine-2-one derivatives have shown interesting results and could be used as model compounds to create novel anti-proliferative drugs. However, more pharmacological evaluation is needed.

Synthesis, spectroscopic analysis, molecular docking and DFT study of novel 1,2,3-Triazole derivatives incorporating paramethoxythymol and salicylaldehyde moieties

This study investigates the synthesis, characterization, and computational analysis of novel paramethoxythymol-1,2,3-triazole derivatives derived from naturally occurring thymol. HRMS and NMR spectroscopy (1H and 13C) were meticulously employed to ensure precise identification of the synthesized compounds. Density functional theory (DFT) calculations were performed to elucidate the stability of the derivatives. In silico docking simulations, molecular dynamics, and ADMET analysis provided insights into the potential interactions between the synthesized molecules and the active sites of Epidermal Growth Factor Receptor (EGFR) and B-cell lymphoma 2 (Bcl2). Docking analysis revealed favorable binding affinities of the 1,2,3-triazole derivatives towards EGFR, with compound 5b exhibiting the most potent interaction, characterized by a docking score of -28.8 kJ/mol. Conversely, compound 6b demonstrated a docking score of -29.2 kJ/mol with Bcl2. Molecular dynamics investigations indicated that the complex between Bcl2 and compound 5b is more stable, suggesting it as a potential candidate for inhibiting Bcl2 protein. These findings suggest that paramethoxythymol-1,2,3-triazole derivatives hold promise as lead candidates for the development of novel targeted anticancer agents.

Synthesis, characterization, anticancer, antibacterial, antioxidant, DFT, and molecular docking of novel La (III), Ce (III), Nd (III), and Dy (III) lanthanide complexes with Schiff base derived from 2‐aminobenzothiazole and coumarin

Four novel lanthanide La (III), Ce (III), Nd (III), and Dy (III) complexes with (Z)‐4‐(benzo[d]thiazol‐2‐ylamino)‐3‐((benzo[d]thiazol‐2‐ylimino)methyl)‐2H‐chromen‐2‐one (L) were prepared and characterized. The novel compounds' structural compositions were elucidated by the application of analytical and spectroscopic methodologies. From physical and chemical measurements, the general formula for the [LnLCl3]2H2O complexes (C1‐C4) was proposed, which was proven by theoretical measurements. Using cisplatin, gentamicin, ampicillin, and ascorbic acid as standards, the compound's anticancer, antibacterial, and antioxidant qualities were assessed, and activities followed the order: Ce (III)L(C2) > Nd (III)L(C3) > Dy (III)L(C4) > La (III)L(C1) > L where the Ce (III) complexes exhibited the highest activity followed by Nd (III) complexes. Molecular docking studies were performed using the MOA2022 software to identify putative binding mechanisms for the methionine adenosyl‐transferases in liver cancer (PDB ID: 5A19) and the most active site of the Bacillus subtilis receptor (PDB ID: 5e6k), where the strength of the interaction increases with the negative binding energy L ˂ [LaLCl3] ˂ [DyLCl3] ˂ [NdLCl3] ˂ [CeLCl3].

Interaction of DisBa01 peptide from Bothrops alternatus venom with BRAF melanoma receptors: Modeling and molecular docking

Metastatic melanoma is highly aggressive and challenging, often leading to a grim prognosis. Its progression is swift, especially when mutations like BRAFV600E continuously activate pathways vital for cell growth and survival. Although several treatments target this mutation, resistance typically emerges over time. In recent decades, research has underscored the potential of snake venoms and peptides as bioactive substances for innovative drugs, including anti-coagulants, anti-microbial, and anti-cancer agents. Leveraging this knowledge, we propose employing a bioinformatics simulation approach to: a) Predict how well a peptide (DisBa01) from Bothrops alternatus snake venom binds to the melanoma receptor BRAFV600E via Molecular Docking. b) Identify the specific peptide binding sites on receptors and analyze their proximity to active receptor sites. c) Evaluate the behavior of resulting complexes through molecular dynamics simulations. d) Assess whether this peptide qualifies as a candidate for anti-melanoma therapy. Our findings reveal that DisBa01 enhances stability in the BRAFV600E melanoma receptor structure by binding to its RGD motif, an interaction absent in the BRAF WT model. Consequently, both docking and molecular dynamics simulations suggest that DisBa01 shows promise as a BRAFV600E inhibitor.

Design, synthesis and molecular modeling of novel D-ring substituted steroidal 4,5-dihydropyrazole thiazolinone derivatives as anti-inflammatory agents by inhibition of COX-2/iNOS production and down-regulation of NF-κB/MAPKs in LPS-induced RAW264.7 macrophage cells

It has been reported that 4,5-dihydropyrazole and thiazole derivatives have many biological functions, especially in the aspect of anti-inflammation. According to the strategy of pharmacophore combination, we introduced thiazolinone and dihydropyrazole moiety into steroid skeleton to design and synthesize a novel series of D-ring substituted steroidal 4,5-dihydropyrazole thiazolinone derivatives, and assessed their in vitro anti-inflammatory profiles against Lipopolysaccharide (LPS)-induced inflammation in RAW 264.7 macrophage cells. The anti-inflammatory activities assay demonstrated that compound 12e was considered as the most effective anti-inflammatory drug, which suppressed the expression of pro-inflammatory mediators including nitric oxide (NO), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α), it also dose-dependently inhibited the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in LPS-induced RAW 264.7 macrophage cells. Furthermore, the results of the Western blot analysis showed a correlation between the inhibition of the Nuclear factor-kappa B (NF-κB) and Mitogen-activated protein kinases (MAPKs) signaling pathways and the suppressive effects of compound 12e on pro-inflammatory cytokines. Molecular docking studies of compound 12e into the COX-2 protein receptor (PDB ID: 5IKQ) active site was performed to rationalize their COX-2 inhibitory potency. The results were found to be in line with the biological findings as they exerted more favorable interactions compared to that of dexamethasone (DXM), explaining their remarkable COX-2 inhibitory activity. The findings revealed that these candidates could be identified as potent anti-inflammatory agents, compound 12e could be a promising drug for the treatment of inflammatory diseases.

Isolation, characterization and pharmacological potentials of methanol extract of Cassia fistula leaves: Evidenced from mice model along with molecular docking analysis

The purpose of the current investigation was to conduct a detailed analysis of the chemical components and medicinal properties of the methanolic crude extract derived from the leaves of Cassia fistula. This analysis was carried out using both experimental (in vivo) and computational (in silico) methods. Eleven chemicals were chromatographically isolated using GC-MS/MS, which utilizes a library of NIST and Wiley 2020 versions. FTIR analysis of the extract was performed to identify the functional group of the compounds. The glucose-lowering capacity, analgesic, and anti-diarrheal activities of methanolic crude extract were analyzed utilizing a well-known oral glucose tolerance test, tail immersion method, writhing assay, and castor oil-induced diarrheal mice methods, respectively. After 60 min, 120 min, and 180 min of loading the drugs, a significant reduction of blood glucose levels was examined (p < 0.05) in all the extracts of this plant (200 mg/kg, 400 mg/kg and 600 mg/kg) utilized in this research at a time-dependent manner. Similarly, all the crude extracts showed significant (p < 0.05) effects against pain centrally and peripherally compared to the standard drug morphine (2 mg/kg bw) and diclofenac sodium (50 mg/kg bw). Moreover, the methanol extract (400 mg/kg bw) manifested anti-diarrheal efficacy by inhibiting 72.0 % of the diarrheal episode in mice compared to the standard drug loperamide (inhibition = 80.0%). The results of the computational investigations corroborated existing in-vivo findings. Greater or close to equivalent binding affinity to the active binding sites of kappa opioid receptor, glucose transporter 3 (GLUT 3), and cyclooxygenase 2 was indicative of the potential anti-diarrheal, hypoglycemic, and analgesic characteristics of the isolated compounds (COX-2). Moreover, anticancer and antimicrobial potentiality was also found impressive through evaluation of binding affinity with epidermal growth factor receptor (EGFR) and dihydrofolate reductase (DHFR) receptors. Results from this study indicated that C. fistula might be a beneficial natural resource for treating diarrhea, hyperglycemia, and pain. However, additional research is required to conduct a comprehensive phytochemical screening and establish precise action mechanisms of the crude extract or the plant-derived compounds.

Design, one-pot novel synthesis of substituted acridine derivatives: DFT, structural characterisation, ADME and anticancer DNA polymerase epsilon molecular docking studies

A novel type of reaction synthesis of an acridine derivative alkaloid of 9-chloro-1-methylacridine-4-carboxylic acid (CMAC) and structurally characterised. FT-IR, 1H NMR, 13C NMR, and GC-mass spectrometry were used. Density functional theory calculations were performed to understand the electronic properties of the molecular structures, including the frontier molecular orbital (FMO), molecular electrostatic potentials (MEP), NLO material properties, RDG studies, and global chemical reactivity descriptors. Furthermore, Theoretical IR, a vibrational wavenumber was obtained for the title compound by simulation and compared with the experimental wavenumbers. Vibrational energy distribution analysis (VEDA) software was used for potential energy decomposition (PED) analysis. Finally, the bioavailability of the title compound was examined by (ADME/Tox) absorption, distribution, metabolism, and excretion properties. DNA polymerase epsilon, which carries a P301R substitution (PDB ID: 6g0a), was used as the receptor for employing an in silico molecular docking process. The docking study revealed the significant interactions between the receptor active sites and the CMAC ligand.

Investigation of the Structural and Electronic Properties of the Novel Synthesized Methyl 2-(2-oxo-2H-chromen-4-ylamino) benzoate Compound by DFT Method and Evaluation of its Anti-Leishmania Agent Potential by Molecular Docking Study

Leishmaniasis is a disease caused by different species of the leishmania parasite, transmitted through the sandfly, within the group of protozoa. According to the World Health Organization, leishmaniasis is one of the most encountered seven tropical diseases. Trypanothione reductase is a vital enzyme for the parasite. This has made Trypanothione reductase a potential target in the treatment of leishmaniasis. The limitations of current therapeutic options and the high cost have increased the motivation for research on the inhibition of Trypanothione reductase. In this study, the structural and electronic properties of the newly synthesized compound methyl 2-(2-oxo-2H-chromen-4-ylamino) benzoate were calculated using DFT/B3LYP and 6-311++G(d,p) basis set. The calculated structural parameters were found to be highly compatible when compared with experimental studies. The crystal packing of the compound was examined through the Hirshfeld surface analysis method. When the potential of the compound to be used as a drug was evaluated using Lipinski criteria, no hindrance to its use in living organisms was found. As the crystal structure of the enzyme was unknown, homology modeling was performed. Finally, in the molecular docking study, the interaction mechanisms of the compound mentioned in the title and the compound clomipramine used as a control in the receptor's active site were examined. The results revealed that the compound mentioned in the title demonstrated a better potential compared to the control compound.

In vitro and in silico studies of the potential cytotoxic, antioxidant, and HMG CoA reductase inhibitory effects of chitin from Indonesia mangrove crab (Scylla serrata) shells

This study aimed to characterize chitin extracted from Indonesia mangrove crab (Scylla serrata) shells, as well as to assess its in vitro cytotoxic, antioxidant, and HMG CoA reductase inhibitory potentials. In silico molecular docking, molecular dynamic, and ADMET prediction analyses were also carried out. Chitin was extracted from mangrove crab shells using deproteination and demineralization processes, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) characterization are then performed. The MTT method was further tested in a study of cell viability, while in vitro method was used to assess HMG CoA reductase inhibitory and antioxidant activities. The extracted chitin was found to have a moderate level of cytotoxic and antioxidant activities. In vitro studies showed that it has an IC50 of 36,65 ± 0,082 μg/mL as an HMG CoA reductase inhibitor, and decreased enzyme activity by 68.733 % at 100 μg/mL as a concentration. Furthermore, in the in silico study, chitin showed a strong affinity to several targets, including HMG CoA reductase, HMG synthase, LDL receptor, PPAR-alfa, and HCAR-2 with binding energies of −5.7; −5.8; −3.6; −5.6; −4.6 kcal/mol, respectively. Based on the ADMET properties, it had non-toxic molecules, which were absorbed and distributed across the blood-brain barrier. The molecular dynamics (MD) simulation also showed that it remained stable in the active sites of HMG CoA reductase receptor for 100 ns. These results indicated that chitin from Indonesian mangrove crab shells can be used to develop more potent HMG CoA reductase inhibitor with antioxidant and cytotoxic activities for effective dyslipidemia therapy.

Synthesis, Characterization, in silico DFT, Molecular docking, ADMET Profiling Studies and Toxicity Predictions of Ag(I) Complex Derived from 4‐Aminoacetophenone

AbstractThe reaction of the synthesized (E)‐1‐(4‐((2,4‐dihydroxy‐6‐methylphenyl)diazenyl)phenyl)ethan‐1‐one, (DMPDE) ligand with Ag(I) ion at room temperature resulted in the formation of the complex; [Ag(DMPDE)(H2O)2]. 1H NMR, 13C NMR, FTIR, UV‐Vis, mass spectra, elemental analyses, thermal analysis (TGA/DTA), and molar conductance measurements were done to elucidate the structure of synthetic compounds. The results revealed an interesting geometrical variation; tetrahedral for Ag(I) complex. FT‐IR spectra demonstrated that the ligand (DMPDE) under investigation behaves as a bidentate ligand (N,O) through the nitrogen atom of the azo group which is the farthest of the acetophenone moiety and oxygen phenolic for benzene moiety and forms a stable five‐membered chelating ring. The electronic structure, molecular electrostatic potential (MEP) and quantum chemical calculations of the newly synthesized compounds are investigated theoretically at the DFT/B3LYP level of theory. Additionally, the ligand (DMPDE) and Ag(I) complex were screened against the growth of pathogenic bacteria [Actinomycosis (G+), E. Escherichia Coli (G−)] and fungi (Penicillium spp.) compared with the reference antibiotics, Chloramphenicol and Nystatin. Furthermore, 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) was used to evaluate the antioxidant activities of the ligand and its complex, which showed they both possess significant antioxidant properties in comparison with L‐ascorbic acid (Vit. C) as standard. Based on docking studies, (DMPDE) and Ag(I) complex demonstrated a greater affinity for (PDB ID: 3T88), which corresponds to Escherichia coli protein (−6.7818 kcal/mol) and (−6.7928 kcal/mol), respectively. Interestingly, the most active Ag(I) complex inside the active site of cervical cancer receptor (PDB ID: 4XR8) demonstrated a higher binding energy (−6.2631 kcal/mol) than free ligand (−5.8561 kcal/mol). In silico, ADMET displayed that compounds obey the Lipinski rule and the “Veber's rule. Consequently, is likely to exhibit oral bioavailability with good LD50 and a safety profile that includes non‐cytotoxicity, non‐immunotoxicity, and non‐skin sensitization. Finally, the compounds synthesized showed significant anticancer activity in human cervical cancer cell lines HeLa and SiHa compared with positive controls (cisplatin) and normal human hepatic cells (WRL‐68). In the present study, all tested cancer cell lines showed promising activity against Ag(I) complex, whose IC50 value ranged from (61.02 to 71.09) μg/mL.

Design of some potent non-toxic Autoimmune disorder inhibitors based on 2D-QSAR, CoMFA, molecular docking, and molecular dynamics investigations

Current clinical research suggests that inhibitors of protein arginine deiminase 4 (PAD4), major histocompatibility complex (MHC) class II HLA-DQ-ALPHA chain, and thyrotropin receptor (or TSH receptor) which are of biological and therapeutic interest, may show potential in treating rheumatoid arthritis, type 1 diabetes, Graves' disease and other autoimmune disorder. In the present study, a comprehensive analysis was conducted on a collection of 32 compounds concerning their anti-rheumatoid arthritis activity as inhibitors of PAD4. This analysis represents the first instance in which these compounds were computationally examined, employing an in-silico approach that considered 2D-3D QSAR modeling, and molecular docking and was further validated through molecular dynamics and ADMET properties assessment. A credible 2D QSAR (Q_LOO^2 ​= ​0.6611 and R^2 ​= ​0.7535) model was constructed and verified using an external validation test set, Y-randomization, variance inflation factor (VIF), mean effect (MF), and William's plot applicability domain (AD). Ligand-based alignment was implemented in the 3D-QSAR examination. The outcomes demonstrated that CoMFA (uvepls) (Q2LOO ​= ​0.5877; R2 ​= ​0.9983) possess remarkable stability and foresight. The internal validation indicated that CoMFA (uvepls) MIFs display superior predictive capability compared to COMFA (ffdsel). Structural criteria determined by the contour maps of the model and molecular docking simulations were strategically employed to computationally develop 10 new, non-toxic autoimmune disease inhibitors with increased efficacy. Docking tests were done on the newly developed compounds to illustrate their binding mechanism and to identify critical interaction residues inside the active region of rheumatoid arthritis (PDB id: 3BLU). In addition, docking results of the selected designed compounds inside the active sites of type 1 diabetes receptor (6DFX), and Graves' disease receptor (4QT5) demonstrated their rheumatoid arthritis (PDB id: 3BLU) selectivity. A molecular dynamics simulation and binding free energy calculations using the MM/GBSA technique confirmed the stability of the proposed compound D4 inside the rheumatoid arthritis (3BLU) receptor active site. In summary, the results of our investigation might give considerable insight into the future design and development of new autoimmune disease inhibitors.

Coumarin-amino acid hybrids as promising anticancer agents: design, synthesis, docking studies and CK2 inhibition.

A series of mono-peptide, di-peptide and tri-peptide derivatives linked to a coumarin scaffold (5a-c, 7a-c, and 9a-c) were synthesized via the azide-coupling method from corresponding hydrazides 4, 6, and 8. These compounds were tested for anticancer activity against HepG-2, PC-3, and Hct-116 cell lines. Compounds, 7c, and 5b showed significant cytotoxicity, outperforming doxorubicin, with IC50 values of 34.07, 16.06, and 16.02 μM for 7c and 42.16, 59.74, and 35.05 μM for 5b. Compound 7b also displayed promising results with IC50 values of 72.13, 70.82, and 61.01 μM. Moreover, the key structural features of amino acids indicated that mono-peptide and di-peptide derivatives play a key role in increasing their anticancer activities compared with tri-peptides. In addition, the most potent compound 5b also exhibited strong CK2 kinase inhibition with an IC50 value of 0.117 ± 0.005 μM compared with roscovetine as a control drug with an IC50 value of 0.251 ± 0.011 μM. Finally, the binding mode of the chemical inhibitors at the active site of CK2 receptor was also investigated using a docking study which confirmed that the presence of the amino acid functionality is an important feature for anticancer activity and the synthesized compounds showed favorable ADME properties. Besides that, SAR analysis was implemented for the target compounds.

Synthesis and Application of a Near-Infrared Light-Emitting Fluorescent Probe for Specific Imaging of Cancer Cells with High Sensitivity and Selectivity.

The preclinical diagnosis of tumors is of great significance to cancer treatment. Near-infrared fluorescence imaging technology is promising for the in-situ detection of tumors with high sensitivity. Here, a fluorescent probe was synthesized on the basis of Au nanoclusters with near-infrared light emission and applied to fluorescent cancer cell labeling. Near-infrared methionine-N-Hydroxy succinimide Au nanoclusters (Met-NHs-AuNCs) were prepared successfully by one-pot synthesis using Au nanoclusters, methionine, and N-Hydroxy succinimide as frameworks, reductants, and stabilizers, respectively. The specific fluorescence imaging of tumor cells or tissues by fluorescent probe was studied on the basis of SYBYL Surflex-DOCK simulation model of LAT1 active site of overexpressed receptor on cancer cell surface. The results showed that Met-NHs-AuNCs interacted with the surface of LAT1, and C_Score scored the conformation of the probe and LAT1 as five. Characterization and in vitro experiments were conducted to explore the Met-NHs-AuNCs targeted uptake of cancer cells. The prepared near-infrared fluorescent probe (Met-NHs-AuNCs) can specifically recognize the overexpression of L-type amino acid transporter 1 (LAT1) in cancer cells so that it can show red fluorescence in cancer cells. Meanwhile, normal cells (H9c2) have no fluorescence. The fluorescent probe demonstrates the power of targeting and imaging cancer cells.

In Silico Activity Prediction and Docking Studies of the Binding Mechanisms of Levofloxacin Structure Derivatives to Active Receptor Sites of Bacterial Type IIA Topoisomerases

The need for new antimicrobial agents (AntAg) is driven by the persistent antibiotic resistance in microorganisms, as well as the increasing frequency of pandemics. Due to the deficiency of AntAg, research aimed at developing speedy approaches to find new drug candidates is relevant. This study aims to conduct an in silico study of the biological activity spectrum as well as the molecular binding mechanisms of four structurally different forms of levofloxacin (Lvf) with bacterial topoisomerases targets of type IIA (DNA gyrase and topoisomerase IV) to enable the development of drugs with an improved characterization of the safety profile. To achieve this goal, a number of software products were used, such as ChemicPen v. 2.6, PyMol 2.5, Avogadro 1.2.0, PASS, AutoDockTools 1.5.7 with the new generation software Autodock Vina. These software products are the first to be made available for visualization of clusters with determination of ligand-receptor pair binding affinity, as well as clustering coordinates and proposed mechanisms of action. One of the real structures of Lvf, a decarboxylated derivative, was obtained with tribochemical (TrbCh) exposure. The action spectrum of molecular ligands is described based on a Bayesian probability activity prediction model (PASS software Version 2.0). Predicted and real (PMS and RMS) molecular structures of Lvf, with decreasing levels of structural complexity, were translated into descriptors via Wiener (W), Balaban (Vs), Detour (Ip), and Electropy € indices. The 2D «structure-activity» diagrams were used to differentiate closely related structures of levofloxacin. PMS and RMS were visualized as 3D models of the ligand-receptor complexes. The contact regions of RMS and PMS with key amino acid residues—SER-79, DT-15, DG-1, DA-1—were demonstrated. The intra- and inter-molecular binding sites, data on free energy (affinity values, kcal/mol), the binding constant Kb (M−1), and the number of clusters are presented. The research results obtained from the presented in silico approach to explore the spectrum of action find quantitative “structure-activity” correlations, and predict molecular mechanisms may be of applied interest for directed drug discovery.

Synthesis, equilibrium, DFT, and docking studies of a homopiperazine complex with dibutyltin(IV)

The interaction of dibutyltin(IV) dichloride (DBT) with 1,4-diazacycloheptane (homopiperazine, HP) was investigated. In solutions, the complexes formed a 1:1 complex, its protonated and hydrolyzed forms. The formation constants of the complexes and thermodynamic parameters as ΔH° and ΔS° were estimated. The optimization of the structure of the (Bu)2Sn(HP)Cl2 complex reveals that the tin is six-coordinate in a distorted octahedral geometry, where the two nitrogen atoms of homopiperazine and the two chloride ions are in one plane. The solid (Bu)2Sn(HP)Cl2 complex with homopiperazine was synthesized, and the composition was assigned by elemental micro-analysis and mass spectrum. The complex was investigated by infrared, mass spectra, and thermal measurements. The ligand and its complex were tested against antimicrobial Staphylococcus aureus (+ve), Escherichia coli (−ve), and antifungal Candida albicans and Aspergillus flavus. Anticancer activities of homopiperazine and its dibutyltin(IV) complex were tested against breast cancer cell lines. The molecular docking investigations were performed to know the possible modes of binding to the most active sites of the breast cancer oxidoreductase receptor and those of Escherichia coli.