In silico and in vitro prediction of new synthesized N-heterocyclic compounds as anti-SARS-CoV-2.

Computer-aided drug design has been employed to get the medicinal effects against Corona virus from different pyridine derivatives after synthesizing the new compounds. Additionally, various computational studies are also employed between the newly prepared pyridine derivatives and three controls against three proteins (6Y2E, 6M71 and 6M3M). Different methods were employed to synthesize new pyridine derivatives according to the literature using different reaction mediums. MTT was performed for cytotoxicity study and IC50 for inhibitory concentration. Additionally, in-silico studies including DFT, molecular docking, molecular dynamics, MMPBSA, ADME, pharmacokinetics and Lipinski rules were evaluated. The chemical structures of all new compounds were elucidated based on spectroscopic investigation. A molecular docking study demonstrated that compounds 5, 11, and 12 have the best binders of the SARS-CoV-2 main protease enzyme, with energy scores of - 7.5 kcal/mol, - 7.2 kcal/mol, and - 7.9 kcal/mol, respectively. The net binding energy values of the 11-Mpro, 12-Mpro, and 5-Mpro complexes revealed their highly stable nature in terms of both intermolecular interactions and docked conformation across the simulation time. ADME properties, besides the pharmacokinetics and Lipinski rules, showed that all seven newly synthesized compounds follow Lipinski rules with high GI absorption. The In Vitro antiviral study against SARS-CoV-2 using MTT methods confirms that compound 5 has more potential and is safer than other tested compounds. The study shows that the newly synthesized pyridine derivatives have medicinal properties against SARS-CoV-2 without violating Lipinski rules. Compounds 5, 11, and 12, particularly compound 5, may serve as promising potential candidate for COVID-19.

A computational investigation of galactopyranoside esters as antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetics, and bioactivity prediction.

One of the most common viral infections worldwide is the Human Papilloma Virus (HPV) which has been linked to cancer and other diseases in many countries. Monosaccharide esters are significant in the field of carbohydrate chemistry because they are efficient in the synthesis of pharmacologically active compounds. Therefore, the present study aimed to perform thermodynamic, molecular docking and molecular dynamics study of a series of previously designed monosaccharaides, methyl ß-d-galactopyranoside (MGP, 1) esters (2-10) with along with their physicochemical and pharmacokinetic properties. We have optimized the MGP esters employing the DFT study at the B3LYP/6-311 + G (d,p) level of theory. The subsequent analysis also investigated the electronic energies, enthalpies, entropies, polarizability, and natural bond orbital (NBO) of these modified esters. Then, MGP esters were docked into CTX-M-15 extended-spectrum beta-lactamase from Escherichia coli (PDB: 4HBT) and E2 DNA-binding domain from human papillomavirus type 31 (PDB: 1A7G), and the results revealed that most of the esters can efficiently bind to the target. Desmond was used to doing molecular dynamics simulations at 200 ns in addition to molecular docking to look at the binding conformational stability of the protein-ligand complex. Based on RMSD and RMSF, it was determined that the stability of the protein-ligand combination was maintained during the whole 200 ns simulations for all compounds. Finally, a pharmacokinetic study suggests that modified esters of MGP exhibited better pharmacokinetic characteristics and were less hazardous than the parent drug. This work demonstrated that potential MGP esters can efficiently bind to 4HBT and 1A7G proteins and opened avenues for the development of newer antimicrobial agents that can target dangerous pathogens.Communicated by Ramaswamy H. Sarma.

Nanoparticles of a Pyrazolo-Pyridazine Derivative as Potential EGFR and CDK-2 Inhibitors: Design, Structure Determination, Anticancer Evaluation and In Silico Studies.

The strategic planning of this study is based upon using the nanoformulation method to prepare nanoparticles 4-SLNs and 4-LPHNPs of the previously prepared 4,5-diphenyl-1H-pyrazolo[3,4-c]pyridazin-3-amine (4) after confirming its structure with single crystal X-ray analysis. These nanoparticles exhibited promising cytotoxic activity against HepG-2, HCT-116 and MCF-7 cancer cell lines in comparison with the reference doxorubicin and the original derivative 4. Moreover, their inhibitory assessment against EGFR and CDK-2/cyclin A2 displayed improved and more favorable impact than the parent 4 and the references. Detection of their influence upon cancer biomarkers revealed upregulation of Bax, p53 and caspase-3 levels and downregulation of Bcl-2 levels. The docking simulation demonstrated that the presence of the pyrazolo[3,4-c]pyridazin-3-amine scaffold is amenable to enclosure and binding well within EGFR and CDK-2 receptors through different hydrophilic interactions. The pharmacokinetic and physicochemical properties of target 4 were also assessed with ADME investigation, and the outcome indicated good drug-like characteristics.

Analysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET.

Natural product such as flavonoids and their derivatives have a discernible capability to inhibit tumor formation and the growth of cancer cell, which have a vital link between diet and chronic disease prevention. Several plants and spices that contain flavonoid derivatives have been used in traditional medicine as disease preventative and therapeutic agents. Therefore, flavonoids could be used as chemotherapeutic drugs, indicating their potential clinical utility in cancer treatment. The purpose of this research was to discover and produce innovative pharmaceuticals from natural sources by introducing structural changes into flavonoids' backbones and changing their structures to improve biological activity and anticancer effects. In the current study, it was expected that the percent unbound values for the 15 compounds in human plasma would be low, ranging between 0.188 and 0.391. However, all compounds have a safe range and are not toxic to the brain. Compounds 2, 10, and 13 were shown to be permeable to the CNS (log PS > -3), but all other compounds had difficulty penetrating the CNS. Furthermore, all compounds had a low total clearance, ranging from 0.038 to 1.216 ml/min/kg, indicating that these compounds have a long half-life. None of the compounds caused skin sensitization (SS), and only compounds 1, 11, and 12 are expected to be AMES-positive, suggesting that the other compounds are not mutagenic. The result of the study showed based on the Drug-likeness and ADMET studies, only 3 compounds, including 3, 4, and 15, have a good pharmacokinetics propriety, the lowest toxicity, and good binding affinity towards Caspase 3 V266APDB (ID: 5I9B) as potential inhibitor candidates for the HeLa cell line, they have a low total clearance property and no AMES mutagenicity or hERG inhibition properties. These compounds (3,4,15) were examined to act as new cytotoxic drug candidates and would have an interest as starting point for designing compounds against the HeLa cell line.Communicated by Ramaswamy H. Sarma.

Design, synthesis, spectroscopic characterization, in-vitro antibacterial evaluation and in-silico analysis of polycaprolactone containing chitosan-quercetin microspheres.

Aim of present study was to synthesize a novel chitosan-quercetin (CTS-QT) complex by making a carbodiimide linkage using maleic anhydride as cross-linker and to investigate its enhanced antibacterial and antioxidant activities as compare to pure CTS and QT. Equimolar concentration of QT and maleic anhydride were used to react with 100 mg CTS to form CTS-QT complex. For this purpose, three bacterial strains namely E. Coli, S. Aureus and P. Aeruginosa were used for in-vitro antibacterial analysis (ZOI, MIC, MBC, checker board and time kill assay). Later molecular docking studies were performed on protein structure of E. Coli to assess binding affinity of pure QT and CTS-QT complex. MD simulations with accelerated settings were used to explore the protein-ligand complex's binding interactions and stability. Antioxidant profile was determined by performing DPPH• radical scavenging assay, total antioxidant capacity (TAC) and total reducing power (TRP) assays. Delivery mechanism to CTS-QT complex was improved by synthesizing polycaprolactone containing microspheres (CTS-QT-PCL-Levo-Ms) using Levofloxacin as model drug to enhance their antibacterial profile. Resulted microspheres were evaluated by particle size, charge, surface morphology, in-vitro drug release and hemolytic profile and are all were found within limits. Antibacterial assay revealed that CTS-QT-PCL-Levo-Ms showed more than two folds increased bactericidal activity against E. Coli and P. Aeruginosa, while 1.5 folds against S. Aureus. Green colored formation of phosphate molybdate complexes with highest 85 ± 1.32% TAC confirmed its antioxidant properties. Furthermore, molecular docking and dynamics studies revealed that CTS-QT was embedded nicely within the active pocket of UPPS with binding energy greater than QT with RSMD value of below 1.5. Conclusively, use of maleic acid, in-vitro and in-silico antimicrobial studies confirm the emergence of CTS-QT complex containing microspheres as novel treatment strategy for all types of bacterial infections.Communicated by Ramaswamy H. Sarma.

Human targeted phenobarbital presents a poor substrate of gut microbiome deciphering new drug targets beyond pharmacokinetic curbs.

BACKGROUND: The gut microbiome, a new organ of the body, can potentially alter the pharmacokinetics of orally administered drugs through microbial enzymes. However, absorption of orally administered non-antibiotic drugs by the gut microbiome, during drug-microbiome interaction, is barely addressed. Structural homology studies confirm similar membrane transport proteins in gut epithelial cells and the gut microbiome of the host that may compete for drug substrates with the host itself for its absorbance. Therefore, it is hypothesized that orally administered human targeted phenobarbital may interact and/or be uptake by the gut microbiome during its transit through the small intestine. METHODS: In the current in vivo study, thirty-six male Wistar albino rats were divided into six groups including one control and 5 treatment groups, each having an equal number of rats (n = 6). Phenobarbital was administered orally (single dose of 15 mg/kg bw) to treatment groups. Animals were subsequently sacrificed to harvest microbial mass pallets residing in the small intestine after 2, 3, 4, 5, and 6 h of phenobarbital administration. Phenobarbital absorbance by the microbiome in the microbial lysate was estimated through RP-HPLC-UV at a wavelength of 207 nm. RESULTS: Maximum phenobarbital absorbance (149.0 ± 5.93 µg) and drug absorbance per milligram of microbial mass (1.19 ± 0.05 µg) were found significantly higher at 4 h of post-administration in comparison to other groups. Percent dose recovery of phenobarbital was 5.73 ± 0.19% at 4 h while the maximum intestinal transit time was 5 h till the drug was absorbed by the microbes. Such results pronounce the idea of the existence of structural homology between membrane transporters of the gut microbiome and intestinal enterocytes of the host that may competitively absorb orally administered phenobarbital during transit in the small intestine. The docking studies revealed that the phenobarbital is a poor substrate for the gut microbiome. CONCLUSION: Gut microbiome may competitively absorb the non-antibiotics such as phenobarbital as novel substrates due to the presence of structurally homologous transporting proteins as in enterocytes. This phenomenon suggests the microbiome as a potential candidate that can significantly alter the pharmacokinetics of drugs.

Self-assembly of new cobalt complexes based on [Co (SCN)4], synthesis, empirical, antioxidant activity, and quantum theory investigations.

The cobalt (II) complexes have been synthesized from the reaction of the cationic entities (3,4-dimethylaniline (1) and histamine (2)) with metallic salt CoCl2⋅6H2O and thiocyanate ion (SCN-) as a ligand in H2O/ethanolic solution and processing by the evaporation crystal growth method at room temperature to get crystals. The synthesized complex has been fully characterized by single-crystal X-ray diffraction. UV-Visible, FTIR spectroscopy, TGA analysis, and DFT circulations were also performed. The crystal structural analysis reveals that the solid (1) {[Co(SCN)4] (C8H12N)3}·Cl crystallizes in the monoclinic system with the space group P21/n and the solid (2) {[Co(SCN)4](C5H11N3)2}·2Cl crystallizes in the monoclinic space group P21/m. Metal cations are joined into corrugated chains parallel to the b-axis direction in (1) and (2) by four thiocyanate anions. The crystal structures of (1) and (2) were calculated using XRPD data, indicating that they are closely connected to the DRX mono-crystal results. Different interactions pack the system into a ring formed by N-H⋯Cl and N-H⋯S hydrogen bonds. C-H⋯π and the π⋯π stacking of anilinuim ring for (1) and N-H⋯S intermolecular interactions for (1) and (2) increase the crystals' robustness. Hirshfeld surface analysis cum 2D fingerprint plots visualize the main intermolecular interactions with their contributions in the solid-state phase. The molecular geometries of both complexes obtained from the crystal structure were used for quantum chemical calculation. Here, frontier orbital analysis and electrostatic potential illustrate the chemical reactivities of metal-organic complexes. QTAIM and NCI analysis reveal the strength of interactions at the electronic level.

New Benzimidazole-, 1,2,4-Triazole-, and 1,3,5-Triazine-Based Derivatives as Potential EGFRWT and EGFRT790M Inhibitors: Microwave-Assisted Synthesis, Anticancer Evaluation, and Molecular Docking Study.

A new series of benzimidazole, 1,2,4-triazole, and 1,3,5-triazine derivatives were designed and synthesized using a microwave irradiation synthetic approach utilizing 2-phenylacetyl isothiocyanate (1) as a key starting material. All the new analogues were evaluated as anticancer agents against a panel of cancer cell lines utilizing doxorubicin as a standard drug. Most of the tested derivatives exhibited selective cytotoxic activity against MCF-7 and A-549 cancer cell lines. Furthermore, the new target compounds 5, 6, and 7 as the most potent antiproliferative agents have been assessed as in vitro EGFRWT and EGFRT790M inhibitors compared to the reference drugs erlotinib and AZD9291. They represented more potent suppression activity against the mutated EGFRT790M than the wild-type EGFRWT. Moreover, the compounds 5, 6, and 7 down-regulated the oncogenic parameter p53 ubiquitination. A docking simulation of compound 6b was carried out to correlate its molecular structure with its significant EGFR inhibition potency and its possible binding interactions within the active site of EGFRWT and the mutant EGFRT790M.

Diagnostic, Prognostic, Predictive, and Monitoring Role of Neutrophil CD11b and Monocyte CD14 in Neonatal Sepsis.

BACKGROUND: Sepsis is a critical medical condition that requires additional diagnostic considerations. Recently, focus has shifted to the diagnosis of sepsis using new markers to overcome the limitations of traditional laboratory diagnostic modalities. Neutrophil CD11b (nCD11b) and monocyteCD14 (mCD14) cell surface antigens have been shown to be useful in such diagnostic consideration. AIM: To investigate the diagnostic, monitoring, prognostic, and predictive roles of nCD11b and mCD14 as sepsis biomarkers in comparison to each other and to traditional laboratory sepsis parameters in order to select the best fit for routine daily use in neonatal intensive care units (NICUs). SUBJECT: The study included 188 neonates from Ain Shams University Hospitals' NICUs, who were divided into two groups: the control group (n = 100) and the sepsis group (n = 88). Highly sensitive CRP (hs-CRP), complete blood count (CBC), blood culture, and nCD11b and mCD14 evaluations were all part of the laboratory sepsis evaluation (done by flow cytometry technology). Positive blood culture results (BACT/ALERT system) confirmed the sepsis diagnosis. Twenty-four enrolled sepsis neonates were subjected to follow-up assessments, and they were divided into two groups based on clinical improvement: improved sepsis and sepsis without improvement. In order to predict performance evaluation, the subjected neonates were reclassified according to their outcome into survivors' and nonsurvivors' group. RESULTS: Sepsis patients had a significant increase in mCD14 MFI values when compared to controls. With sensitivity 75.4 percent, specificity 71.9 percent, efficacy 73.3 percent, and AUC 0.703, mCD14 MFI at cutoff 9.36 could distinguish the presence of septicemia. Significant increases in both mCD14 MFI and nCD11b MFI (P = 0.001) were observed in the severe sepsis/septic shock group compared to the nonsevere sepsis group. The combined measurement of CD14 MFI at cutoff 9.97 and CD14 percent at cutoff 44.7 percent yielded the best predictive performance. CONCLUSION: Sepsis patients had a significant increase in mCD14 MFI comparable to the controls. mCD14 MFI demonstrated better diagnostic, prognostic, and predictive results than nCD11b. hs-CRP outperformed mCD14 and nCD11b in terms of diagnostic efficacy and AUC. In the monitoring of sepsis patients, both mCD14 and nCD11b produced unsatisfactory results. Currently, the routine use of mCD14 or nCD11b as sepsis biomarkers in neonatal ICUs is not justified.

The Utility of Neutrophil CD64 and Presepsin as Diagnostic, Prognostic, and Monitoring Biomarkers in Neonatal Sepsis.

BACKGROUND: Neonatal septicemia is a critical medical situation; current conventional laboratory methods still have many limitations and diagnostic obstacles. For this purpose, last decades have witnessed a challenge between the battery of sepsis biomarkers including many leukocyte surface antigens, not only for early diagnostic purposes but also for better follow-up and good management of sepsis patients. AIM: To evaluate the diagnostic, prognostic, and monitoring performance of both neutrophil CD64 (nCD64) and presepsin as sepsis biomarkers compared to each other and to the conventional laboratory sepsis parameters aiming to decide which is the best fitting for routine daily use in neonatal intensive care units (NICUs). METHODS: 235 neonates were enrolled from three Egyptian neonatal ICUs, during the period from November 2015 till March 2018; they were classified into two main groups: the control group (n = 102) and the sepsis group (n = 133). Laboratory sepsis evaluation included highly sensitive CRP (hs-CRP), CBC, in addition to nCD64 (flow cytometry technique), and presepsin measurement (CLEIA technique combined with Magtration® technology); the diagnosis was confirmed thereafter by positive blood culture results (BacT/Alert system). Sixty-two of the enrolled sepsis neonates were subjected to follow-up assessment; they were reclassified according to their clinical improvement at the second time assessment into (group 1: sepsis group without improvement) (n = 20) and (group 2: improved sepsis group) (n = 42). RESULTS: Significant increase in nCD64 and presepsin values was found in sepsis groups compared to the controls. At cutoff 41.6%, nCD64% could discriminate the presence of septicemia with sensitivity 94.7%, specificity 93.6 %, and AUC 0.925, while presepsin at cutoff 686 pg/ml achieves sensitivity 82.7%, specificity 95.5%, and AUC 0.887, respectively. Significant increase in nCD64 (P < 0.001) and hs-CRP (P=0.018) values was observed in severe sepsis/septic shock patients compared to nonsevere sepsis patients. Delta change percentage (dC%) between initial and follow-up evaluations for both improved and nonimproved sepsis patients was dC Z value -5.904 for nCD64% followed by dC Z value -4.494 for presepsin. CONCLUSION: nCD64 and presepsin are valuable early diagnostic and monitoring sepsis biomarkers; the highest sensitivity could be achieved by a univariant sepsis marker in this study was recorded by the nCD64% biomarker, while the highest specificity was documented by presepsin. Combined measurement of both achieves the highest diagnostic performance in sepsis neonates. Either of CD64 or presepsin combined with hs-CRP associated with better performance than any of them alone. nCD64 carries an additional promising role in reflecting sepsis prognosis.

Valuable Role of Neutrophil CD64 and Highly Sensitive CRP Biomarkers for Diagnostic, Monitoring, and Prognostic Evaluations of Sepsis Patients in Neonatal ICUs.

BACKGROUND: Neonatal sepsis (NS) is a very critical medical situation associated with high morbidities and mortalities. There is an utmost need for a new tool helping in early diagnosis and proper management of sepsis neonates. Neutrophil CD64 (nCD64) shows a very promising value in this concerning issue. AIM: Evaluate the diagnostic, monitoring, and prognostic performances of nCD64 and highly sensitive CRP (hs-CRP) in NS as well as the possible best panel of biomarkers that can achieve the most desirable results. METHODS: Patients were enrolled from three neonatal intensive care units (NICUs) (n = 121 patients) and classified according to their initial sepsis evaluation into three groups: disease control group (n = 30), proven sepsis group (n = 17), and clinical sepsis group (n = 74). Laboratory evaluation included hs-CRP, complete blood count (CBC), and blood culture in addition to nCD64 (done by flow cytometry technique). Besides the diagnostic evaluations, follow-up evaluations were done for 40 patients after five days from the first time; patients were reclassified according to their outcome into the improved sepsis neonates' group (n = 26) and sepsis neonates without improvement (n = 14). RESULTS: Significant increase in nCD64 and hs-CRP results were present in sepsis groups compared to the disease controls (P < 0.001); nCD64 at 43% cutoff value could detect the presence of sepsis with 85.6% sensitivity and 93% specificity. Additionally, delta change percentage (dC%) between improved sepsis neonates and sepsis neonates without improvement showed a significant difference in the levels of both nCD64 (P < 0.001) and hs-CRP (P = 0.001). CONCLUSION: Besides the promising diagnostic performance documented by nCD64 which is higher than the other laboratory sepsis biomarkers used routinely in NICUs, nCD64 has a valuable role in sepsis patients' monitoring and prognostic evaluation. hs-CRP was moderate in its diagnostic and monitoring results being less than that achieved by nCD64. Combined measurement of nCD64% and hs-CRP gives better diagnostic and monitoring performance than that achieved by any of them alone.

Synthesis, Antimicrobial Activity and Molecular Docking of Novel Thiourea Derivatives Tagged with Thiadiazole, Imidazole and Triazine Moieties as Potential DNA Gyrase and Topoisomerase IV Inhibitors.

To develop new antimicrobial agents, a series of novel thiourea derivatives incorporated with different moieties 2-13 was designed and synthesized and their biological activities were evaluated. Compounds 7a, 7b and 8 exhibited excellent antimicrobial activity against all Gram-positive and Gram-negative bacteria, and the fungal Aspergillus flavus with minimum inhibitory concentration (MIC) values ranged from 0.95 ± 0.22 to 3.25 ± 1.00 µg/mL. Furthermore, cytotoxicity studies against MCF-7 cells revealed that compounds 7a and 7b were the most potent with IC50 values of 10.17 ± 0.65 and 11.59 ± 0.59 µM, respectively. On the other hand, the tested compounds were less toxic against normal kidney epithelial cell lines (Vero cells). The in vitro enzyme inhibition assay of 8 displayed excellent inhibitory activity against Escherichia coli DNA B gyrase and moderate one against E. coli Topoisomerase IV (IC50 = 0.33 ± 1.25 and 19.72 ± 1.00 µM, respectively) in comparison with novobiocin (IC50 values 0.28 ± 1.45 and 10.65 ± 1.02 µM, respectively). Finally, the molecular docking was done to position compound 8 into the E. coli DNA B and Topoisomerase IV active pockets to explore the probable binding conformation. In summary, compound 8 may serve as a potential dual E. coli DNA B and Topoisomerase IV inhibitor.