Lessons for fragment library design: analysis of output from multiple screening campaigns

Over the past 8 years, we have developed, refined and applied a fragment based discovery approach to a range of protein targets. Here we report computational analyses of various aspects of our fragment library and the results obtained for fragment screening. We reinforce the finding of others that the experimentally observed hit rate for screening fragments can be related to a computationally defined druggability index for the target. In general, the physicochemical properties of the fragment hits display the same profile as the library, as is expected for a truly diverse library which probes the relevant chemical space. An analysis of the fragment hits against various protein classes has shown that the physicochemical properties of the fragments are complementary to the properties of the target binding site. The effectiveness of some fragments appears to be achieved by an appropriate mix of pharmacophore features and enhanced aromaticity, with hydrophobic interactions playing an important role. The analysis emphasizes that it is possible to identify small fragments that are specific for different binding sites. To conclude, we discuss how the results could inform further development and improvement of our fragment library. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification,synthesis and evaluation of CSF1R inhibitors using fragment based drug design

Colony-stimulating factor 1 receptor is a type III receptor protein tyrosine kinase belonging to PDGFR family. CSF1R signaling is essential for differentiation, proliferation and survival of macrophages. Aberrant expression of CSF1R appears to be an attractive target in several cancer types. Higher expression of CSF1R ligands correlates to tumor progression. CSF1R inhibitors have been shown to suppress cancers. We have attempted an in silico fragment derived drug discovery approach by screening ˜25,000 in-house compounds as potential CSF1R inhibitors. Using FBDD approach we have identified six diverse fragments that exhibit affinity towards hinge region of CSF1R. Some of the fragments 5-nitroindole and 7-azaindole and their derivatives were synthesized for further evaluation. The in silico and in vitro enzyme activity studies reveal moderate inhibition of CSF1R kinase activity by 5-nitroindole and good inhibition by 7-azaindole fragments. Bio and chemiinformatics studies have shown that 7-azaindole compounds have better membrane permeability and enzyme inhibition properties. Molecular docking studies show that the amino acid residues 664–666 in the hinge region of the cytosolic domain of CSF1R to be the preferred region of binding for nitroindole and azaindole derivatives. Further optimization and biological analysis would identify these fragments as potential and promising leads as CSF1R inhibitors.     

Synthesis,biological evaluation,and computational studies of novel fused six-membered O-containing heterocycles as potential acetylcholinesterase inhibitors

An efficient, borax-catalyzed protocol for the synthesis of novel 4-aryl-substituted-4H-pyran derivatives fused to α-pyrone ring in a one-pot is described. By this achievement, some novel 4-aryl substituted 4H-pyrans fused to the α-pyrone ring as potential acetylcholinesterase inhibitors (AChEIs) with good to excellent yields are obtained from a one-pot three-component reaction between various aryl aldehydes, 4-hydroxy-6-methyl-2H-pyran-2-one and malononitrile. The method is a facile, inexpensive, practical and highly efficient one to obtain target compounds. The chemical structures of all compounds were characterized by FT-IR, FT-¹³CNMR and FT-¹HNMR, MS spectroscopy and also elemental analyses data. Furthermore, the purity of all novel compounds was checked by HPLC. In addition, both molecular modelling studies and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMETox) prediction nominated all compounds as good acetylcholinesterase inhibitors to the potential treatment of Alzheimer, Parkinson and Autism diseases that among them compound 4f showed the best activity against acetylcholinesterase enzyme.     

Synthesis and in vitro antimycobacterial potential of novel hydrazones of eugenol

Fifty one hydrazone derivatives of eugenol were designed and docked with 2NSD and 2X22 (enzymes of H37Rv strain) using Schrodinger v7.4. The selective ten hydrazone derivatives (4, 5, 11, 18, 30, 34, 35, 37, 42, and 45) of eugenol were synthesized via esterification, hydrazination and treatment with different aldehydes. Synthesized compounds were characterized by IR, ¹H NMR, and LCMS data. The compounds were evaluated for their antitubercular potential against H37Rv using microplate alamar blue assay (MABA). The study revealed that all synthesized compounds were significantly active at concentration 50 and 100 μg/ml, whereas compound 11 exhibited activity at 25 μg/ml. Present study showed that antitubercular activity of novel hydrazone derivatives of eugenol is strongly connected with the position of the substituent on aromatic aldehyde or ketones.     

Design of compound libraries for fragment screening

Approaches to the design of libraries for fragment screening are illustrated with reference to a 20 k generic fragment screening library and a 1.2 k generic NMR screening library. Tools and methods for library design that have been developed within AstraZeneca are described, including Foyfi fingerprints and the Flush program for neighborhood characterization. It will be shown how Flush and the BigPicker, which selects maximally diverse sets of compounds, are used to apply the Core and Layer method for library design. Approaches to partitioning libraries into cocktails are also described.     

Aluminum chloride-functionalized silica gel synthesis as a catalyst for the preparation of biologically active oxazolidinethiones: Antioxidant and molecular docking studies

The aim of this research paper was the preparation of aluminum chloride bonded to silica gel catalyst and its application in the modification of steroidal molecules. Steroidal oxazolidinethiones were prepared using silica-supported aluminum chloride (SiO₂-AlCl₃) under Microwave irradiation, which is common in organic synthesis to achieve high yields in shorter reaction times. The advantage of this method is that the usual procedure can be carried out without tiring and without a secondary product at the end of the reaction. Physicochemical techniques were used to identify the chemical structure of the prepared oxazolidinethiones. A rationalization of the conversion pathways from steroidal epoxides to oxazolidinethiones is sketched on the basis of current and previous results. Antioxidant activities i.e. DPPH assay, total antioxidant capacity and total reductive capability were performed for steroidal compounds, including reactants, and the results indicated that steroidal oxazolidinethione with acetoxy group had a promising activity among the tested steroids. In correlation with antioxidant activity, a promising steroid derivative was subjected to a molecular docking study for binding to tyrosine kinases, the target protein and showed a negative binding energy −7.8 Kcal/mol suggesting good affinity to the active pocket and can be considered as a better antioxidant in the biological system.     

Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition

Fat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors by applying scaffold hopping approach. Using this novel scaffold, different derivatives were designed by extending scaffold structure with potential functional groups. Molecular docking simulations were carried out by using two different docking algorithm implemented in CDOCKER (flexible docking) and AutoDock programs (rigid docking). Analyzing results of rigid and flexible docking, compound MU06 was selected based on different properties and predicted binding affinities for further analysis. Molecular dynamics simulation of FTO/MU06 complex was performed to characterize structure rationale and binding stability. Certainly, Arg96 and His231 residue of FTO protein showed stable interaction with inhibitor MU06 throughout the production dynamics phase. Three residues of FTO protein (Arg96, Asp233, and His231) were found common in making H-bond interactions with MU06 during molecular dynamics simulation and CDOCKER docking.     

In-silico profiling,design, molecular docking computation,and drug kinetic model evaluation of novel curcumin derivatives as potential anticancer agents

The alarming trend of leukemia cell lines that are multidrug-resistant has prompted scientists to scramble for effective new anticancer treatments. Therefore, it remains an intriguing scientific task to optimize curcumin by trying to introduce molecular alteration to its vital structure to improve the biological effect against the P388 cell line or get around resistance phenomena. Regardless of the wide range of medications that are now being studied, Prednisone remains the most important and efficient part of chemotherapy that the WHO recommends. This article discusses the QSAR-oriented model and in silico assessment of some potent curcumin derivatives' anticancer activity against the P388 cell line. The solidity and propensity for prediction of the model were ensured by using stringent validation procedures. The activity of these derivatives was shown to be unrelated to lipophilicity, while shorter N-N distances and short substituents result in quite bioactive molecules. This information was used to design potent molecules that demonstrate good quality as per the assessment based on the Lead-Like Soft rule is acceptable for drug-like molecules. Also, molecule d2 does not possess any toxic effects risk alerts, suggesting drug-adherent conduct. While Prednisone the reference drug has a toxicity risk alert in red, suggesting non-adherent conduct for Prednisone. Hence, the novel molecules are promising anticancer agents.     

Identification of novel Plasmodium falciparum PI4KB inhibitors as potential anti-malarial drugs: Homology modeling,molecular docking and molecular dynamics simulations

The current study was set to discover selective Plasmodium falciparum phosphatidylinositol-4-OH kinase type III beta (pfPI4KB) inhibitors as potential antimalarial agents using combined structure-based and ligand-based drug discovery approach. A comparative model of pfPI4KB was first constructed and validated using molecular docking techniques. Performance of Autodock4.2 and Vina4 software in predicting the inhibitor-PI4KB binding mode and energy was assessed based on two Test Sets: Test Set I contained five ligands with resolved crystal structures with PI4KB, while Test Set II considered eleven compounds with known IC50 value towards PI4KB. The outperformance of Autodock as compared to Vina was reported, giving a correlation coefficient (R²) value of 0.87 and 0.90 for Test Set I and Test Set II, respectively. Pharmacophore-based screening was then conducted to identify drug-like molecules from ZINC database with physicochemical similarity to two potent pfPI4KB inhibitors –namely cpa and cpb. For each query inhibitor, the best 1000 hits in terms of TanimotoCombo scores were selected and subjected to molecular docking and molecular dynamics (MD) calculations. Binding energy was then estimated using molecular mechanics–generalized Born surface area (MM-GBSA) approach over 50 ns MD simulations of the inhibitor-pfPI4KB complexes. According to the calculated MM-GBSA binding energies, ZINC78988474 and ZINC20564116 were identified as potent pfPI4KB inhibitors with binding energies better than those of cpa and cpb, with ΔG_binding ≥ −34.56 kcal/mol. The inhibitor-pfPI4KB interaction and stability were examined over 50 ns MD simulation; as well the selectivity of the identified inhibitors towards pfPI4KB over PI4KB was reported.     

Synthesis,characterization of Uranyl(VI), Th(IV), Zr(IV) mixed-ligand complexes with S-methyl-2-(4-methoxybenzylidine)dithiocarbazate and N-donor co-ligand,and their evaluation as antimicrobial agent

Schiff base, S-methyl-2-(4-methoxybenzylidine) dithiocarbazate as a primary ligand (HL₁), quinoline (L₂) as a co-ligand, and hydrated metal salts have been reacted in ethanol in 1:2:1 M ratio to produce mixed-ligand complexes of the type, [M(L₁)(L₂)].NO₃ [M = Uranyl(VI), Th(VI), Zr(IV)], The isolated products have been structurally investigated by elemental analyses, ¹H NMR, IR and UV–Vis studies. The electronic studies shows octahedral geometry for all the studied complexes, whereas the molar conductance data suggest an ionic nature. Density functional computation (DFT) studies are also carried out in order to determine the bonding inside the structure of the complexes. The studied mixed-ligand complexes showed moderate antibacterial activity when evaluated against four pathogenic bacteria: Shigella dysenteriae, Bacillus subtilis, Agrobacterium tumefaciens, and Escherichia coli. In addition, molecular docking analysis for all the complexes, using the CLC Drug Discovery Workbench software, showed that they virtually docked on S. dysenteriae, B. subtilis, A. tumefaciens, and E. coli.     

Design,synthesis and computational evaluation of a novel intermediate salt of N-cyclohexyl-N-(cyclohexylcarbamoyl)-4-(trifluoromethyl) benzamide as potential potassium channel blocker in epileptic paroxysmal seizures

The narrow therapeutic range and limited pharmacokinetics of available Antiepileptic drugs (AEDs) have raised serious concerns in the proper management of epilepsy. To overcome this, the present study attempts to identify a candidate molecule targeting voltage gated potassium channels anticipated to have superior pharmacological than existing potassium channel blockers. The compound was synthesized by reacting (S)-(+)-2,3-dihydro-1H-pyrrolo[2,1-c][1,4] benzodiazepine5,11(10H,11aH)-dione with 4-(Trifluoromethyl) benzoic acid (C₈H₅F₃O₂) in DMF and N,N′-dicyclohexylcarbodiimide (DCC) which lead to the formation of an intermediate salt of N-cyclohexyl-N-(cyclohexylcarbamoyl)-4-(trifluoromethyl)benzamide with a perfect crystalline structure. The structure of the compound was characterized by FTIR, ¹H NMR and ¹³C NMR analysis. The crystal structure is confirmed by single crystal X-ray diffraction analysis. The Structure-Activity Relationship (SAR) studies revealed that substituent of fluoro or trifluoromethyl moiety into the compound had a great effect on the biological activity in comparison to clinically used drugs. Employing computational approaches the compound was further tested for its affinity against potassium protein structure by molecular docking in addition, bioactivity and ADMET properties were predicted through computer aided programs.     

Synthesis,characterization and evaluation of novel benzothiazole clubbed chromene derivatives for their anti-inflammatory potential

Abstract

A series of chromene derivatives (5a–f) were prepared by multistep synthesis process using 2-[3-phenyl prop-2-ene nitrile] 1,3-benzothiazole and dimedone using piperidine as catalyst in ethanol. The reaction was found to proceed via Knoevenagel condensation of aldehydes with benzothiazole, followed by the elimination to afford the 2-(benzo[d]thiazol-2-yl)-3-(aryl)acrylonitrile, which then undergoes Michael addition with 5,5-dimethyl-1,3-cyclohexanedione, followed by intramolecular O-cyclization to give the products. The structures of all novel constructed derivatives were corroborated by elemental analysis and spectral data (FT-IR, ¹H-NMR, ¹³C-NMR and Mass). Subsequently, the compounds were tested for their in-vivo anti-inflammatory activity. This study revealed that these synthesized derivatives tend to have significantly anti inflammatory activity and shall prove as structural templates in the design and development of new anti inflammatory drugs.     

Synthesis and biological evaluation of novel thalidomide analogues as potential anticancer drugs

In search of novel anticancer agents, a series of thalidomide analogs （6a-j） were designed and synthesized. Cytotoxicity of these compounds against human hepatoma cells （HepG2） was evaluated by MTT method. Compounds 6d, 6h and 6i showed significant cytotoxic activities comparable to or stronger than control 5-fluorouracil.     

Design,synthesis and evaluation of novel dehydroabietic acid-dithiocarbamate hybrids as potential multi-targeted compounds for tumor cytotoxicity

In the present study, novel representatives of the important group of biologically-active, dehydroabietic acid-bearing dithiocarbamate moiety, were synthesized and characterized by ¹H NMR, ¹³C NMR, HR-MS. The in vitro antiproliferative activity evaluation (MTT) indicated that these compounds exhibited potent inhibitory activities in various cancer cell lines (HepG-2, MCF-7, HeLa, T-24, MGC-803). Particularly, compound III-b possessed extraordinary cytotoxicity with low micromolar IC₅₀ values ranging from 4.07 to 38.84 µM against tested cancer cell lines, while displayed weak cytotoxicity on two normal cell lines (LO-2 and HEK 293 T). Subsequently, the potential mechanisms of representative compound III-b were elementarily investigated by Transwell experiment, which showed III-b can inhibit cancer cells migration. Annexin-V/PI dual staining showed that the compound can induce HepG-2 cells apoptosis in a dose-dependent manner. Meanwhile this apoptosis may be related to the upregulated protein expression of cleaved-caspase 3, cleaved-caspase 9, Bax and downregulated of Bcl-2 indicated by Western Blot. Later study further confirmed that ROS levels in HepG-2 cells increased significantly with the rise of concentrations. In addition, through the network pharmacology data analyzing, the core targets and signaling pathways of compound III-b for treatment of liver neoplasms were forecasted. Molecular docking model showed that compound III-b had high affinity with hub targets (CASP3, EGFR, HSP90AA1, MAPK1, ERBB2, MDM2), suggesting that compound III-b might target the hub protein to modulate signaling activity. Taken together, these data indicated that dehydroabietic acid structural modification following the “Molecular hybridization” principle is a feasible way to discover the potential multi-targeted antitumor compounds.     

Silyl modification of biologically active compounds. 12. Silyl group as true incentive to antitumour and antibacterial action of choline and colamine analogues

A series of triorganylsilyl(β‐dialkylaminoethoxy)silanes was prepared and characterized by elemental analysis, ¹H, ¹³C, ²⁹Si NMR and mass spectroscopy. Comparative study of ²⁹Si resonance of newly synthesized compounds showed correlation between its value and substituent nature at the silicon atom, and is shifted upfield for β‐triorganyl(N,N‐dialkylaminoethoxy)silanes in comparison with corresponding methiodides, revealing weak N^…Si interaction for proper silanes. In vitro antitumour and antimicrobial properties were investigated. The biological activity data exhibited a marked enhancement of inhibitory activity on trialkylsilylation against tumour cell lines and all the test bacterial/fungal strains. Copyright © 2006 John Wiley & Sons, Ltd.     

Synthesis of new racemic and optically active N‐phosphonoalkyl bicyclic β‐amino acids via the kabachnik–fields reaction as potential biologically active compounds

Novel racemic and optically active constrained N‐phosphonoalkyl bicyclic β‐amino acids have been synthesized via the Kabachnik–Fields reaction of the (RS) or (R)‐1‐aminobicyclo[2.2.2]octane‐2‐carboxylic acids with paraformaldehyde and benzaldehyde, and the dimethyl‐H‐phosphonate. The structure of obtained compounds was characterized by NMR (¹H, ¹³C, and ³¹P), LC/MS, and X‐ray diffraction analyses. © 2012 Wiley Periodicals, Inc. Heteroatom Chem 23:123–130, 2012; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20759     

Design and Synthesis of Coumarin Derivatives as Cytotoxic Agents through PI3K/AKT Signaling Pathway Inhibition in HL60 and HepG2 Cancer Cells

In this study, a series of coumarin derivatives, either alone or as hybrids with cinnamic acid, were synthesized and evaluated for their cytotoxicity against a panel of cancer cells using the MTT assay. Then, the most active compounds were inspected for their mechanism of cytotoxicity by cell-cycle analysis, RT-PCR, DNA fragmentation, and Western blotting techniques. Cytotoxic results showed that compound (4) had a significant cytotoxic effect against HL60 cells (IC₅₀ = 8.09 µM), while compound (8b) had a noticeable activity against HepG2 cells (IC₅₀ = 13.14 µM). Compounds (4) and (8b) mediated their cytotoxicity via PI3K/AKT pathway inhibition. These results were assured by molecular docking studies. These results support further exploratory research focusing on the therapeutic activity of coumarin derivatives as cytotoxic agents.