Sobia Ahsan Halim

Synthesis of novel inhibitors of β-glucuronidase based on benzothiazole skeleton and study of their binding affinity by molecular docking.

Benzothiazole derivatives 1-26 have been synthesized and their in vitro β-glucuronidase potential has been evaluated. Compounds 4 (IC(50)=8.9 ± 0.25 μM), 5 (IC(50)=36.1 ± 1.80 μM), 8 (IC(50)=8.9 ± 0.38 μM), 13 (IC(50)=19.4 ± 1.00 μM), 16 (IC(50)=4.23 ± 0.054 μM), and 18 (IC(50)=2.26 ± 0.06 μM) showed β-glucuronidase activity potent than the standard (d-saccharic acid 1,4-lactone, IC(50)=48.4 ± 1.25 μM). Compound 9 (IC(50)=94.0 ± 4.16 μM) is found to be the least active among the series. All active analogs were also evaluated for cytotoxicity and none of the compounds showed any cytotoxic effect. Furthermore, molecular docking studies were performed using the gold 3.0 program to investigate the binding mode of benzothiazole derivatives. This study identifies a novel class of β-glucuronidase inhibitors.

Synthesis of novel derivatives of oxindole, their urease inhibition and molecular docking studies

We synthesized a series of novel 5-24 derivatives of oxindole. The synthesis started from 5-chlorooxindole, which was condensed with methyl 4-carboxybezoate and result in the formation of benzolyester derivatives of oxindole which was then treated with hydrazine hydrate. The oxindole benzoylhydrazide was treated with aryl acetophenones and aldehydes to get target compounds 5-24. The synthesized compounds were evaluated for urease inhibition; the compound 5 (IC50 = 13.00 ± 0.35 μM) and 11 (IC50 = 19.20 ± 0.50 μM) showed potent activity as compared to the standard drug thiourea (IC50 = 21.00 ± 0.01 μM). Other compounds showed moderate to weak activity. All synthetic compounds were characterized by different spectroscopic techniques including (1)H NMR, (13)C NMR, IR and EI MS. The molecular interactions of the active compounds within the binding site of urease enzyme were studied through molecular docking simulations.

In silico and in vitro immunomodulatory studies on compounds of Lindelofia stylosa.

Lindolefia stylosa (Kar. and Kir.) is an important medicinal plant in Central and West Asia. Compounds 1 (ethyl lithospermate), 2 (methyl lithospermate), 3 (lithospermate B), 4 (rosmarinic acid), 5 (methyl rosmarinate), 6 (ethyl rosmarinate), 7 (3‐O‐feruloyl‐6′‐O‐coumaroyl sucrose), 8 (3‐O‐feruloyl‐6′‐O‐caffeoyl sucrose), 9 (3,6′‐O‐diferuloyl sucrose), 10 (3,6′‐O‐diferuloyl‐1‐kestose), 11 (3‐O‐feruloyl‐6′‐O‐coumaroyl‐1‐kestose), 12 (3,6′‐O‐diferuloyl nystose), 13 (3‐O‐Feruloyl‐6′‐O‐coumaroyl nystose), 14 (p‐coumaric acid), 15 (ferulic acid), 16 (naphthalene glycoside (8‐O‐β‐D‐glucopyranoside)), and 17 (4′‐hydroxy‐5‐methoxy‐6,7‐methylenedioxyisoflavone), isolated from this plant, were evaluated for their ability to modulate the immune response. Studies included monitoring the effect on reactive oxygen species (ROS) production, T‐lymphocyte proliferation, and inhibition of four cytokines (IL‐2, TNFα, IL‐1β, and IL‐4). These cytokines play a major role in immune response modulation. Molecular docking studies on selected compounds were also conducted, which predict a potent activity of compounds 5 and 6 and moderate activity of compounds 1 and 2 as inhibitors of IL‐2. Correlation between the predicted binding scores and the experimental results was found to be valid. Compound 5 was identified as the most potent IL‐2 inhibitor in the series.

Immunosuppressive Activity of Buxidin and E‐Buxenone from Buxus hyrcana

Buxidin (1) and E‐Buxenone (2), steroidal alkaloids from Buxus hyrcana, are found to possess potent immunosuppressive properties. The activity was tested in vitro on oxidative burst, chemotaxis, T‐cell proliferation, and cytokine production. Both compounds showed a significant immunomodulatory activity with clear suppressive effect on oxidative burst and chemotaxis in a dose‐dependent manner. They also exhibited suppressive effect on the phytohemagglutinin‐stimulated T‐cell proliferation. The immunomodulatory activity was further confirmed by the suppression of IL‐2 and IL‐4 production. Furthermore, molecular docking studies were performed to investigate the binding mode of Buxidin (1) and E‐Buxenone (2) with IL‐2. Despite the structural differences between Buxidin (1) and E‐Buxenone (2), docking results revealed that they adopt a similar binding pattern at the active site of the IL‐2. A good agreement between practical and theoretic results indicates that the current docking study could provide an alternate tool for the structural optimization of recently identified ligand as more potent IL‐2 inhibitors.

Synthesis, biological evaluation, and molecular docking studies of benzyl, alkyl and glycosyl [2-(arylamino)-4,4-dimethyl-6-oxo-cyclohex-1-ene] carbodithioates, as potential immunomodulatory and immunosuppressive agents

The immunomodulating properties of functionalized [2-(arylamino)-4,4-dimethyl-6-oxo-cyclohex-1-ene] carbodithioates and 6,6-dimethyl-4-(2-(propan-2-ylidene)hydrazinyl)-6,7-dihydro-2H-indazole-3(5H)-thione compounds have been investigated. Four of them, 13, 18, 19 and 20 inhibited PBMC proliferation induced by phytohemagglutinin (PHA) in a dose dependent manner with an IC(50) of ≤ 20 μM. The Th-1 cytokine, interleukin-2 (IL-2) in PHA/PMA-stimulated peripheral blood mononuclear cells (PBMCs) is significantly inhibited by 13, 19 and 20 with an IC(50) of 8.4 ± 0.4, 5.34 ± 0.15 and 4.9 ± 0.7 μM, respectively. They also inhibited the PMA/lipopolysaccharide-induced proinflammatory cytokines, IL-1β and TNF-α production in human monocytic leukemia cells (THP-1), by 86%, 46% and 59.2% for IL-1β and by 83.8%, 48.2% and 58.7% for TNF-α, respectively. Only 20 showed significant suppressive activity against the phagocyte oxidative burst in a dose dependent manner, with an IC(50) of 23.8 μM. LPS-induced nitrites in mouse macrophages were found to be inhibited by compounds 6, 8, 13-15 and 19 with an IC(50), which range between 7.7 and 63 μM. The cytotoxicity for the active compounds was also studied on Rat Wistar Hepatocyte cell line, CC1 and the Mouse Fibroblast cell line 3T3 NIH in the presence of compounds using a standard MTT assay. Furthermore, structural-activity relationship using automated docking software revealed that active compounds 7, 13 and 19, adapted the same binding mode, however the most active compound 20 is found deeply inserted within the ligand binding site of IL-2, as multiple hydrophobic and hydrophilic key interactions stabilize the compound inside the binding site, thus contributing higher activity.

The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies

Benzothiazole and its natural or synthetic derivatives have been used as precursors for several pharmacological agents for neuroprotective, anti-bacterial, and anti-allergic activities. The objective of the present study was to evaluate effects of benzothiazole analogs (compounds 1-26) for their immunomodulatory activities. Eight compounds (2, 4, 5, 8-10, 12, and 18) showed potent inhibitory activity on PHA-activated peripheral blood mononuclear cells (PBMCs) with IC50 ranging from 3.7 to 11.9 μM compared to that of the standard drug, prednisolone <1.5 μM. Some compounds (2, 4, 8, and 18) were also found to have potent inhibitory activities on the production of IL-2 on PHA/PMA-stimulated PBMCs with IC50 values ranging between <4.0 and 12.8 μM. The binding interaction of these compounds was performed through silico molecular docking. Compounds 2, 8, 9, and 10 significantly suppressed oxidative burst ROS production in phagocytes with IC50 values between <4.0 and 15.2 μM. The lipopolysaccharide (LPS)-induced nitrites in murine macrophages cell line J774 were found to be inhibited by compounds 4, 8, 9, and 18 at a concentration of 25 μg/mL by 56%, 91%, 58%, and 78%, respectively. Furthermore, compounds 5, 8, 12, and 18 showed significant (P<0.05) suppressive activity on Th-2 cytokine, interleukin 4 (IL-4) with an IC50 range of <4.0 to 40.3 μM. Interestingly compound 4 has shown a selective inhibitory activity on IL-2 and T cell proliferation (naïve T cell proliferation stage) rather than on IL-4 cytokine, while compound 12 displayed an interference with T-cell proliferation and IL-4 generation. Moreover compound 8 and 18 exert non-selective inhibition on both IL-2 and IL-4 cytokines, indicating a better interference with stage leading to humoral immune response and hence possible application in autoimmune diseases.

Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations.

Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) methods. Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models. The best CoMFA and CoMSIA models were obtained with the AM1 charges when used with co-conformer based substructure alignment (CCBSA) method. The obtained models posses excellent correlation coefficient value and also exhibited good predictive power (for CoMFA: q(2)=0.619; r(2)=0.890; r(2)Pred=0.765 and for CoMSIA: q(2)=0.607; r(2)=0.884; r(2)Pred=0.655). The developed models were further validated by using a set of another sixteen compounds as external test set 2 and both models showed strong predictive power with r(2)Pred=>0.8. The contour maps obtained from these models better interpret the structure activity relationship; hence the developed models would help to design and optimize more potent IL-2 inhibitors. The results might have implications for rational design of specific anti-inflammatory compounds with improved affinity and selectivity.

A combined 3D-QSAR and docking studies for the In-silico prediction of HIV-protease inhibitors

BackgroundTremendous research from last twenty years has been pursued to cure human life against HIV virus. A large number of HIV protease inhibitors are in clinical trials but still it is an interesting target for researchers due to the viral ability to get mutated. Mutated viral strains led the drug ineffective but still used to increase the life span of HIV patients.ResultsIn the present work, 3D-QSAR and docking studies were performed on a series of Danuravir derivatives, the most potent HIV- protease inhibitor known so far. Combined study of 3D-QSAR was applied for Danuravir derivatives using ligand-based and receptor-based protocols and generated models were compared. The results were in good agreement with the experimental results. Additionally, docking analysis of most active 32 and least active 46 compounds into wild type and mutated protein structures further verified our results. The 3D-QSAR and docking results revealed that compound 32 bind efficiently to the wild and mutated protein whereas, sufficient interactions were lost in compound 46.ConclusionThe combination of two computational techniques would helped to make a clear decision that compound 32 with well inhibitory activity bind more efficiently within the binding pocket even in case of mutant virus whereas compound 46 lost its interactions on mutation and marked as least active compound of the series. This is all due to the presence or absence of substituents on core structure, evaluated by 3D-QSAR studies. This set of information could be used to design highly potent drug candidates for both wild and mutated form of viruses.

3D Structure Prediction of Human β1-Adrenergic Receptor via Threading-Based Homology Modeling for Implications in Structure-Based Drug Designing

Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1). This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein.

Attempt to Explore the Binding Mechanism of IL-1ò Inhibitors viaMolecular Docking Studies

IL-1β is an important cytokineinvolved in several immune responses. IL-1β exerts its effect by binding with its receptorcalled IL-1R1 and leading to a series of intra-cellular signalling. The over-expression of IL-1β leads to immunological complications including arthritis and auto-immune disorders. Currently there are several drugs in the market to cure the inflammation either by inhibiting the production of IL-1β or affecting its signal cascade. The hindrance in the interaction between IL-1β interaction and its receptor can stop its function hence hope to cure inflammatory diseases. This study presents a docking analysis of five commercially available drugs at the IL-1β/IL-1R1 protein interface. This study would give an insight for designing the drugs, capable to block the direct interaction of IL-1β with its receptor ultimately leading to some more consistent cure for inflammatory diseases.