Letters in Drug Design & Discovery - Volume 16, Issue 6, 2019

Background: Peroxisome proliferator-activated receptor gamma (PPARγ) is one of the key targets of insulin resistance research, in addition to being ligand-activated transcription factors of the nuclear hormone receptor superfamily with a leading role in adiposeness activation and insulin sensitivity. They regulate cholesterol and carbohydrate metabolism through direct actions on gene expression. Despite their therapeutic importance, there are dose limiting side effects associated with PPARγ drug treatments, thus a new generation of safer PPARγ drugs are being actively sought after treatment. Methods: In this study, we used computer aided drug design to screen new series of PPARγ ligands, and synthesized a series of potential thiazolidinedione derivatives such as 5,7- dibenzyloxybenzyl-3-hydroxymethyl-4H-coumarin-4-ketone, using 4-steps to synthesize the target compounds and built streptozotocin (STZ) induced insulin resistance rat model to measure their antidiabetic activity. Results: We found that 10 mg/kg concentration of compound 0701C could significantly decrease blood glucose and serum PPARγ, serum insulin levels in insulin resistance model rat. Conclusion: We would conclude that compound 0701C might serve as a potential PPARγ partial agonist.

Background: The development of drug-resistant by bacteria appears rapidly and thus making the effectiveness of antibiotics severely limited. Methods: A series of thiourea derivatives was synthesized, characterized and evaluated for their in vitro antibacterial, antifungal and antiviral activities. Results: Structures of the newly synthesized compounds were confirmed by elemental and spectral analysis. The biological results showed that some of the target compounds displayed comparable antimicrobial and antiviral activities with reference drugs. Structure-activity relationship studies revealed that the ortho- chloro or fluoro substituted phenyl at Ar1 and substituted pyridinyl at Ar2 positions of the thiourea nucleus are essential for their in vitro antimicrobial and anti-HIV activity. In particular, compounds 8 and 10 showed better activity against the tested bacteria, fungi and viral strains than other synthesized PET derivatives reported in the present study. Conclusion: These results provide an encouraging lead that could be used for the development of new potent antiviral and antimicrobial agents.

Background: Capecitabine is one of the most effective and successful drugs for the treatment of uterine and colorectal cancer which has been limited in use due to occurrence of handfoot syndrome (HFS). Overexpression of human thymidine phosphorylase enzyme is predicted to be one of the main causes of this syndrome. Thymidine phosphorylase enzyme is involved in many cancers and inflammatory diseases and pyrimidine nucleoside phosphorylase family is found in a variety of organisms. Results of clinical studies have shown that topical usage of henna plant (Lawsonia inermis from the family of Lythraceae) could reduce the severity of HFS. Methods: By using in silico methods on reported compounds of henna, the present study is aimed at finding phytochemicals and chemical groups with the potential to efficiently interact with and inhibit human thymidine phosphorylase. Various compounds (825) of henna from different chemical groups (138) were virtually screened by the interface to AutoDock in YASARA Software package, against the enzyme structure obtained from X-ray crystallography and refined by homology modeling methods. Results: By virtual screening, i.e. docking of candidate ligands into the determined active site of hTP, followed by applying the scoring function of binding affinity, 71 compounds (out of 825 compounds) were estimated to have the likelihood to bind to the protein with an interaction energy higher than 10 kcal/mol (Concerning the sign of “binding energies”, please refer to the Methods section). Conclusion: Finally, diosmetin-3'-O-β-D-glucopyranoside (#219) and monoglycosylated naphthalene were respectively selected as the most potent phytochemicals and chemical groups. Flavonoid-like compounds with appropriate interaction energy were also considered as the most probable inhibitors. More investigations on henna compounds, are needed in order to approve their effectiveness and also to explore more anti-cancer, anti-inflammatory, anti-angiogenesis and even antibiotics.

Background: N-myc downstream regulated gene 3 (NDRG3) is a newly discovered oxygen-regulated protein which will bind with L-Lactate in hypoxia and further activate Raf (rapidly accelerated fibrosarcoma)-ERK (extracellular regulated protein kinases) pathway, promoting cell growth and angiogenesis. Methods: Competitive inhibition on the binding of NDRG3 and L-Lactate may be potentially a useful strategy for the repression of hypoxic response mediated by NDRG3. The threedimensional (3D) structure of NDRG3 was built by using homology modeling for its crystal structure was not available. Then, L-Lactate was docked into NDRG3, from which we knew it bound with amino acid residues Gln69, His183, Asn189, Ala72 and Pro66 of NDRG3 in the most possible active sites. Approximately 3000 compounds have been virtually screened and the 6 topranked compounds were selected as reference molecules to analyze their interaction relationships, which illustrated that some of them might form electrostatic interaction with Glu70 and Asp187, π-π stack with Phe75 and Tyr180, hydrogen bonds with Gly71 and Asn189, hydrophobic effect with Ala72 and Ile184. Results: Novel molecules were designed through structural optimization of the 6 top-ranked compounds and subsequently their ADMET properties were predicted. Conclusion: These molecules may be potential drug candidates for the suppression of hypoxic response mediated by NDRG3 and targeted therapy for hypoxia-induced diseases.

Background: In this study, novel ortho-hydroxy N-acyl hydrazone moiety including compounds (3a-l) were designed, based on procaspase activating compound (PAC-1) which is a small molecule known with antitumor activity. The antitumor activity was evaluated on A549 (human lung cancer cell line) and CCD 19Lu (human lung normal cell line). Methods: Twelve N'-arylidene-2-[4-(methylsulfonyl)piperazin-1-yl]acetohydrazide derivatives (3a-l) were synthesized starting from ethyl 1-piperazinylacetate. All compounds were tested using MTT method and Xcelligence-Real time cell analysis system (RTCA DP) to determine their antitumor activity. Results: Some physicochemical properties of four active compounds were also predicted using MolSoft, PreADMET and PROTOX software. Four of them, 3h, 3j, 3k and 3l bearing 3-hydroxy, 4-dimethylamino, 2,6-dichloro and 3,4-dichloro substituents in order exhibited selective cytotoxicity. Conclusion: Eligible values were obtained in the specified ranges as to be an oral/intravenous drug considering the physicochemical calculations.

Background: In search of novel anticancer agents, a series of 1,3,4-oxadiazole derivatives (12a-j) containing 1,3,4-thiadiazole moieties were synthesized, and their structures were confirmed by 1HNMR, 13CNMR and ESI-MS spectral analysis. Methods: Cytotoxicity of these compounds was evaluated by MTT assay in vitro against four human tumor cell lines, i.e. A549 (lung), MCF-7 (breast), A375 (melanoma) and HT-29 (colon). Results: Here, CA4 used as positive control. Among them, compounds 12b, 12c, 12f, 12g, 12h and 12j were exhibited promising activity than control drug. Conclusion: In conclusion, we have synthesized a novel series of 1,3,4-oxadiazole fused 1,3,4- thiazdiazole derivatives and their structures were confirmed by spectral analysis.

Background: Three series of new 7-fluoro-4-(1-piperazinyl) quinolines (I1~I6, II1~II2 and IV1~IV4) were synthesized. Their anti-tumor activity was evaluated in vitro against three human carcinoma cell lines, namely SGC-7901 cells, BEL-7402 cells and A549 cells expressing high levels of EGFR by Methyl Thiazolyl Terazolium (MTT) assay. Methods: Three series of quinoline derivatives were synthesized, characterized and evaluated for their in vitro anti-tumor activities. Results and Discussion: Structures of the newly synthesized compounds were confirmed by spectral analysis. The preliminary bioassay indicated that compounds I1, I10 and II1 exhibited better anti-tumor activity than the rest of the target compounds and gefitinib against A549 cell based assay, which demonstrated that compounds I1, I10 and II1 are potential agents for cancer therapy. Results suggested that the substitutes on piperazinyl influenced anti-tumor activities remarkably. Conclusion: These results are useful for discovering more potent novel anti-tumor compounds and further studies are ongoing.

Background: Large-scale energy landscape characterization of protein-protein interactions (PPIs) is important to understand the interaction mechanism and protein-protein docking methods. The experimental methods for detecting energy landscapes are tedious and the existing computational methods require longer simulation time. Objective: The objective of the present work is to ascertain the energy profiles at the interface regions in a rapid manner to analyze the energy landscape of protein-protein interactions. Methods: The atomic coordinates obtained from the X-ray and NMR spectroscopy data are considered as inputs to compute cumulative energy profiles for experimentally validated protein-protein complexes. The energies computed by the program were comparable to the standard molecular dynamics simulations. Results: The PPI Profiler not only enables rapid generation of energy profiles but also facilitates the detection of hot spot residue atoms involved therein. Conclusion: The hotspot residues and their computed energies matched with the experimentally determined hot spot residues and their energies which correlated well by employing the MM/GBSA method. The proposed method can be employed to scan entire proteomes across species at an atomic level to study the key PPI interactions.

Background: SMS family plays a very important role in sphingolipids metabolism and is involved in the membrane mobility and signaling transduction. Methods: SMS2 subtype was related to a variety of diseases and could be regarded as a promising potential drug target. However, the uncertainty of the binding sites and the molecular mechanism of action limited the development of SMS2 inhibitors. Herein, we discovered a photo-affinity probe PAL-1 targeting SMS2. Results: The enzyme inhibitory activity and the photo-affinity labeling experiments showed that PAL-1 could be mono-labeled on SMS2. Conclusion: In summary, starting from the N-arylbenzamides core structure and the minimalist terminal alkyne-containing diazirine photo-crosslinker, we designed and synthesized a photoaffinity probe PAL-1 targeting SMS2. The enzymatic inhibitory activity study showed that PAL-1 exhibited superior selectivities for SMS2 with an IC50 of 0.37 μM over SMS1.

Background: In this study; we aimed to increase water solubility and formula dissolution through synthesizing more soluble chemical derivative of rutin. Objective: The synthesized rutin derivative is novel and shows an improvement in solubility and hence possibly a better oral bioavailability. The steps followed in this study are of major benefit which can be utilized by herbal and pharmaceutical industries to improve their products. Methods: In this study, a selective partial acetylation was performed to produce a hexaacetylated ester of rutin. Water solubility of the synthesized hexaacetylated ester of rutin and its dissolution were tested and compared to the original rutin. A simple UV/Vis spectrophotometric method was developed and validated. Results: Water solubility and dissolution profile of hexaacetylated ester derivative of rutin were increased by approximately two folds compared to that of the original rutin. The antioxidant activity of the synthesized derivative was comparable to original rutin. The developed analytical method was found to be linear, accurate, precise, robust and capable of quantifying the active ingredient at low concentration (0.0259 mg/ml). Conclusion: An improvement in the solubility of rutin was achieved. The tablet formulation of the partially acetylated ester derivative of rutin gives a better dissolution over the marketed rutin tablets.

Background: 1,2,3-Triazoles and imidazoles are important five-membered heterocyclic scaffolds due to their extensive biological activities. These products have been an area of growing interest to many researchers around the world because of their enormous pharmaceutical scope. Methods: The in vivo and in vitro enzyme inhibition of some thioglycosides encompassing 1,2,4- triazole N1, N2, and N3 and/or imidazole moieties N4, N5, and N6. The effect on the antioxidant enzymes (superoxide dismutase, glutathione S-transferase, glutathione peroxidase and catalase) was investigated as well as their effect on α-glucosidase and β-glucuronidase. Molecular docking studies were carried out to investigate the mode of the binding interaction of the compounds with α- glucosidase and β -glucuronidase. In addition, quantitative structure-activity relationship (QSAR) investigation was applied to find out the correlation between toxicity and physicochemical properties. Results: The decrease of the antioxidant status was revealed by the in vivo effect of the tested compounds. Furthermore, the in vivo and in vitro inhibitory effects of the tested compounds were clearly pronounced on α-glucosidase, but not β-glucuronidase. The IC50 and Ki values revealed that the thioglycoside - based 1,2,4-triazole N3 possesses a high inhibitory action. In addition, the in vitro studies demonstrated that the whole tested 1,2,4-triazole are potent inhibitors with a Ki magnitude of 10-6 and exhibited a competitive type inhibition. On the other hand, the thioglycosides - based imidazole ring showed an antioxidant activity and exerted a slight in vivo stimulation of α-glucosidase and β- glucuronidase. Molecular docking proved that the compounds exhibited binding affinity with the active sites of α -glucosidase and β-glucuronidase (docking score ranged from -2.320 to -4.370 kcal/mol). Furthermore, QSAR study revealed that the HBD and RB were found to have an overall significant correlation with the toxicity. Conclusion: These data suggest that the inhibition of α-glucosidase is accompanied by an oxidative stress action.