Development of energetic pharmacophore for the designing of 1,2,3,4-tetrahydropyrimidine derivatives as selective cyclooxygenase-2 inhibitors

We present here the Energetic pharmacophore model representing complementary features of the 1,2,3,4-tetrahydropyrimidine for selective cyclooxygenase-2 (COX-2) inhibition. For the development of pharmacophore hypothesis, a total of 43 previously reported compounds were docked on active site of COX-2 enzyme. The generated pharmacophore features were ranked using energetic terms of Glide XP docking for 1,2,3,4-tetrahydropyrimidine scaffold to optimize its structure requirement for COX-2 inhibition. The thirty new 4,5,6-triphenyl-1,2,3,4-tetrahydropyrimidine derivatives were synthesized and assessed for selective COX-2 inhibitory activity. Two compounds 4B1 and 4B11 were found to be potent and selective COX-2 inhibitors. The molecular docking studies revealed that the newly synthesized compounds can be docked into COX-2 binding site and also provide the molecular basis for their activity.     

Pose prediction accuracy in docking studies and enrichment of actives in the active site of GSK-3beta

We present molecular docking studies on the inhibitors of GSK-3beta kinase in the enzyme binding sites of the X-ray complexes (1H8F, 1PYX, 1O9U, 1Q4L, 1Q5K, and 1UV5) using the Schr?dinger docking tool Glide. Cognate and cross-docking studies using standard precision (SP) and extraprecision (XP) algorithms have been carried out. Cognate docking studies demonstrate that docked poses similar to X-ray poses (root-mean-square deviations of less than 2 A) are found within the top four ranks of the GlideScore and E-model scores. However, cross-docking studies typically produce poses that are significantly deviated from X-ray poses in all but a couple of cases, implying potential for induced fit effects in ligand binding. In this light, we have also carried out induced fit docking studies in the active sites of 1O9U, 1Q4L, and 1Q5K. Specifically, conformational changes have been effected in the active sites of these three protein structures to dock noncognate ligands. Thus, for example, the active site of 1O9U has been induced to fit the ligands of 1Q4L, 1Q5K, and 1UV5. These studies produce ligand docked poses which have significantly lower root-mean-square deviations relative to their X-ray crystallographic poses, when compared to the corresponding values from the cross-docking studies. Furthermore, we have used an ensemble of the induced fit models and X-ray structures to enhance the retrieval of active GSK-3beta inhibitors seeded in a decoy database, normally used in Glide validation studies. Thus, our studies provide valuable insights into computational strategies useful for the identification of potential GSK-3beta inhibitors.     

Novel and Potential Small Molecule Scaffolds as DYRK1A Inhibitors by Integrated Molecular Docking-Based Virtual Screening and Dynamics Simulation Study

The dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a novel, promising and emerging biological target for therapeutic intervention in neurodegenerative diseases, especially in Alzheimer’s disease (AD). The molMall database, comprising rare, diverse and unique compounds, was explored for molecular docking-based virtual screening against the DYRK1A protein, in order to find out potential inhibitors. Ligands exhibiting hydrogen bond interactions with key amino acid residues such as Ile165, Lys188 (catalytic), Glu239 (gk+1), Leu241 (gk+3), Ser242, Asn244, and Asp307, of the target protein, were considered potential ligands. Hydrogen bond interactions with Leu241 (gk+3) were considered key determinants for the selection. High scoring structures were also docked by Glide XP docking in the active sites of twelve DYRK1A related protein kinases, viz. DYRK1B, DYRK2, CDK5/p25, CK1, CLK1, CLK3, GSK3β, MAPK2, MAPK10, PIM1, PKA, and PKCα, in order to find selective DYRK1A inhibitors. MM/GBSA binding free energies of selected ligand–protein complexes were also calculated in order to remove false positive hits. Physicochemical and pharmacokinetic properties of the selected six hit ligands were also computed and related with the proposed limits for orally active CNS drugs. The computational toxicity webserver ProTox-II was used to predict the toxicity profile of selected six hits (molmall IDs 9539, 11352, 15938, 19037, 21830 and 21878). The selected six docked ligand–protein systems were exposed to 100 ns molecular dynamics (MD) simulations to validate their mechanism of interactions and stability in the ATP pocket of human DYRK1A kinase. All six ligands were found to be stable in the ATP binding pocket of DYRK1A kinase.     

Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation

We have developed a method that uses energetic analysis of structure-based fragment docking to elucidate key features for molecular recognition. This hybrid ligand- and structure-based methodology uses an atomic breakdown of the energy terms from the Glide XP scoring function to locate key pharmacophoric features from the docked fragments. First, we show that Glide accurately docks fragments, producing a root mean squared deviation (RMSD) of <1.0 Å for the top scoring pose to the native crystal structure. We then describe fragment-specific docking settings developed to generate poses that explore every pocket of a binding site while maintaining the docking accuracy of the top scoring pose. Next, we describe how the energy terms from the Glide XP scoring function are mapped onto pharmacophore sites from the docked fragments in order to rank their importance for binding. Using this energetic analysis we show that the most energetically favorable pharmacophore sites are consistent with features from known tight binding compounds. Finally, we describe a method to use the energetically selected sites from fragment docking to develop a pharmacophore hypothesis that can be used in virtual database screening to retrieve diverse compounds. We find that this method produces viable hypotheses that are consistent with known active compounds. In addition to retrieving diverse compounds that are not biased by the co-crystallized ligand, the method is able to recover known active compounds from a database screen, with an average enrichment of 8.1 in the top 1% of the database.     

Synthesis,anticancer, molecular docking and QSAR studies of benzoylhydrazone

To find out effective anticancer compounds we synthesized (1–30) derivatives of 4-isopropylbenzoylhydrazone and evaluated for anticancer potential. The compounds 3, 9, 12, 23, 26 and 28 showed better activities ranging (0.39–1.1 µg/ml) than the standard (1.53 ± 0.01 µg/ml). In line with this, compounds 2, 6, 24, 25 and 29 exhibited better activities compared to the second standard (5FU 4.60 ± 0.01 µg/ml). The best molecular docked complex between the BRCA1 structure and the 1–30 derivatives were analyzed based on the Glide docked score and binding orientation for both the SP and XP mode. The 2D-QSAR analysis reflected a significant correlation between the experimental and the predicted biological activities. The above-mentioned compounds were also assessed by various spectroscopic techniques.     

Artificial intelligence-aided discovery of prolyl hydroxylase 2 inhibitors to stabilize hypoxia inducible factor-1α and promote angiogenesis

From ZINC database with a total of 1.8 million small molecules, four compounds are identified as prolyl hydroxylase 2 inhibitors through a virtual screening workflow that sequentially incorporates machine learning, molecular docking, and molecular dynamics. Among them, compound 103, (E)-5-(5-((2-(1H-tetrazol-5-yl)hydrazineylidene)methyl)furan-2-yl)isoindoline-1,3-dione, promotes the migration and capillary tube formation capacity of human umbilical vein endothelial cells through enhancing the stability of hypoxia inducible factor-1α and increasing the level of vascular endothelial growth factor.     

Discovery of a Prenylated Flavonol Derivative as a Pin1 Inhibitor to Suppress Hepatocellular Carcinoma by Modulating MicroRNA Biogenesis

Peptidyl‐prolyl cis‐trans isomerase Pin1 plays a crucial role in the development of human cancers. Recently, we have disclosed that Pin1 regulates the biogenesis of miRNA, which is aberrantly expressed in HCC and promotes HCC progression, indicating the therapeutic role of Pin1 in HCC therapy. Here, 7‐(benzyloxy)‐3,5‐dihydroxy‐2‐(4‐methoxyphenyl)‐8‐(3‐methylbut‐2‐en‐1‐yl)‐4H‐chromen‐4‐one ( AF‐39 ) was identified as a novel Pin1 inhibitor. Biochemical tests indicate that AF‐39 potently inhibits Pin1 activity with an IC₅₀ values of 1.008 μm , and also displays high selectivity for Pin1 among peptidyl prolyl isomerases. Furthermore, AF‐39 significantly suppresses cell proliferation of HCC cells in a dose‐ and time‐dependent manner. Mechanistically, AF‐39 regulates the subcellular distribution of XPO5 and increases miRNAs biogenesis in HCC cells. This work provides a promising lead compound for HCC treatment, highlighting the therapeutic potential of miRNA‐based therapy against human cancer.     

Identification of novel HDAC8 selective inhibitors through ligand and structure based studies: Exploiting the acetate release channel differences among class I isoforms

Histone deacetylases (HDACs) are key regulators of gene expression and have emerged as crucial therapeutic targets for cancer. Among the HDACs, inhibition of HDAC8 enzyme has been reported to be a novel strategy in the treatment of female-specific cancers. Most of the HDAC inhibitors discovered so far inhibit multiple HDAC isoforms causing toxicities in the clinic thus limiting their potential. Therefore, the discovery of isoform-selective HDAC8 inhibitors is highly desirable. In the present study, a combination of ligand and structure based drug design tools were utilized to build a statistically significant pharmacophore based 3D QSAR model with statistical parameters R²: 0.9964, and Q²: 0.7154, from a series of 31 known HDAC8 inhibitors. Top 1000 hits obtained from Virtual screening of Phase database were subjected to docking studies against HDAC8. Top 100 hits obtained were redocked into HDAC Class I (HDAC 1,2,3) and Class II isoforms (HDAC 4, 6) and rescored with XP Glide Score. Based on fitness score, XP glide score and interacting amino acid residues, five HDAC8 inhibitors (1–5) were selected for in vitro studies. The HDAC8 activity assay followed by enzyme kinetics clearly indicated Compounds 1, 2 and 3 to be potent HDAC8 selective inhibitors with IC₅₀ of 126 pM, 112 nM, and 442 nM respectively. These compounds were cytotoxic to HeLa cells where HDAC8 is overexpressed but not to normal cells, HEK293. Also, they were able to induce apoptosis by modulating Bax/Bcl2, cleavage of PARP and release of Cytochrome C. Molecular Dynamics simulations observed most favorable interaction patterns and presented a rationale for the activities of the identified compounds. Selectivity against HDAC8 was due to exploitation of the architectural difference in the acetate release channel among class I HDAC isoforms.     

Synthesis of 5-deoxy-5-phospho-d-ribonohydroxamic acid: a new competitive and selective inhibitor of type B ribose-5-phosphate isomerase from Mycobacterium tuberculosis

5-Deoxy-5-phospho-d-ribonohydroxamic acid, a mimic of the 1,2-cis-enediolate high-energy intermediate species of the allose-6-phosphate isomerase reaction, was obtained by a six-step synthesis from d-erythronolactone. In contrast to the known competitive ribose-5-phosphate isomerase (Rpi) inhibitors 4-deoxy-4-phospho-d-erythronohydroxamic acid, 4-deoxy-4-phospho-d-erythronate, and 4-deoxy-4-phosphonomethyl-d-erythronate, the new hydroxamic acid selectively inhibits Mycobacterium tuberculosis RpiB (K_i = 0.40 mM, K_m/K_i = 4.5) versus Spinacia oleracea RpiA, and hence appears as a promising lead for the design of potent species-specific inhibitors of the bacterial enzyme.     

Novel spiroannulated 3-benzofuranones. Synthesis and inhibition of the human peptidyl prolyl cis/trans isomerase Pin1

The novel 3H-spiro[1-benzofuran-2-cyclopentan]-3-one skeleton has been made accessible by different routes. One- and two-step protocols lead to tricyclic and tetracyclic benzofuranones 2 and 3, respectively. A four-step synthesis to spirocompound 4 is described. The novel spirocyclic benzofuranones display modest to no inhibition of the human peptidyl prolyl cis/trans isomerase Pin1.     

Looking glass mechanism-based inhibition of peptidylglycine α-amidating monooxygenase

Carboxyl-terminal amidation, a required post-translational modification for the bioactivation of many peptide hormones, entails sequential enzymatic action by peptidylglycine α-monooxygenase (PAM, EC 1.14.17.3) and peptidylamidoglycolate lyase (PGL, EC 4.3.2.5). We have previously demonstrated that PAM and PGL exhibit strict tandem reaction stereospecificities, with PAM producing exclusively α-hydroxyglycine moieties of absolute configuration (S), and PGL being reactive only toward (S)-α-hydroxyglycines, and we have also shown that PAM exhibits strict P₂-subsite stereospecificity toward both peptide substrates and peptidyl competitive inhibitors. Herein, it is reported that the inhibitory stereochemistry of olefinic mechanism-based amidation inhibitors differs from the strict subsite stereospecificity exhibited by PAM toward substrates and reversible competitive inhibitors. Kinetic analyses of mechanism-based irreversible inhibition of PAM by the (S)- and (R)-enantiomers of 5-acetamido-4-oxo-6-phenyl-2-hexenoic acid were carried out using the rigorous progress curve method. The two enantiomers were found to exhibit very similar values of K_I and k_inact and in both cases kinetic analysis confirmed that irreversible inhibition occurs strictly at the substrate binding site with no ESI complex being formed during the catalytic processing of these irreversible inhibitors. Molecular docking studies were carried out to help rationalize the sharp contrast in the stereospecificity of PAM toward irreversible inhibitors versus substrates and competitive inhibitors. The results revealed that, in contrast to substrates, both docked enantiomers of the olefinic irreversible inhibitors are well-positioned to undergo catalytic processing at the Cu center that gives rise to irreversible inhibition. Taken together, these results provide one of the first clear examples where the stereospecificity of a particular enzyme toward mechanism-based irreversible inhibitors differs from that for substrates and competitive inhibitors.     

Identification of Druggable Targets for Acinetobacter baumannii Via Subtractive Genomics and Plausible Inhibitors for MurA and MurB

Emergence of the multidrug-resistant pathogens has rendered the current therapies ineffective thereby, resulting in the need for new drugs and drug targets. The accumulating protein sequence data has initiated a drift from classical drug discovery protocols to structure-based drug designing. In the present study, in silico subtractive genomics approach was implemented to find a set of potential drug targets present in an opportunist bacterial pathogen, Acinetobacter baumannii (A. baumannii). Out of the 43 targets identified, further studies for protein model building and lead-inhibitor identification were carried out on two cell-essential targets, MurA and MurB enzymes (of A. baumannii designated as MurA_Ab and MurB_Ab) involved in the peptidoglycan biosynthesis pathway of bacteria. The homology model built for each of them was further refined and validated using various available programs like PROCHECK, Errat, ProSA energy plots, etc. Compounds showing activity against MurA and MurB enzymes of other organisms were collected from the literature and were docked into the active site of MurA_Ab and MurB_Ab enzymes. Three inhibitors namely, T6361, carbidopa, and aesculin, showed maximum Glide score, hydrogen bonding interactions with the key amino acid residues of both the enzymes and acceptable ADME properties. Furthermore, molecular dynamics simulation studies on MurA_Ab–T6361 and MurB_Ab–T6361 complexes suggested that the ligand has a high binding affinity with both the enzymes and the hydrogen bonding with the key residues were stable in the dynamic condition also. Therefore, these ligands have been propsed as dual inhibitors and promising lead compounds for the drug design against MurA_Ab and MurB_Ab enzymes.     

Crystallographic proof for an extended hydrogen-bonding network in small prolyl isomerases

Parvulins compose a family of small peptidyl-prolyl isomerases (PPIases) involved in protein folding and protein quality control. A number of amino acids in the catalytic cavity are highly conserved, but their precise role within the catalytic mechanism is unknown. The 0.8 ? crystal structure of the prolyl isomerase domain of parvulin Par14 shows the electron density of hydrogen atoms between the D74, H42, H123, and T118 side chains. This threonine residue has previously not been associated with catalysis, but a corresponding T152A mutant of Pin1 shows a dramatic reduction of catalytic activity without compromising protein stability. The observed catalytic tetrad is strikingly conserved in Pin1- and parvulin-type proteins and hence constitutes a common feature of small peptidyl prolyl isomerases.     

Identification of Novel β3-Adrenoceptor Agonists Using Energetic Analysis, Structure Based Pharmacophores and Virtual Screening

β3 Adrenergic receptor (β3-AR), is a potential therapeutic target for the treatment of type II diabetes and obesity. We report the identification of novel compounds as β3-AR agonists by integrating different approaches of energetic analysis, structure based pharmacophore designing and virtual screening. In a step wise filtering protocol, structure based virtual screening of 2,33,450 compounds was done. These molecules were docked into the active site of the receptor utilizing three levels of accuracy; ligands passing the HTVS (high throughput virtual screening) step were subsequently analyzed in Glide SP (Standard Precision) and finally in Glide XP (Extra Precision) to estimate the receptor ligand binding affinities. In the second step a total of 300 pharmacophore hypotheses were generated from a set of known and diverse β3-AR agonists. The best hypothesis showed six features: three hydrogen bond acceptors, one positively charged group, and two aromatic rings. To cross validate, pharmacophore filtering was done on the set of shortlisted compounds from structure based VS (virtual screening). The different screening techniques employed were validated using enrichment factor calculations. The energetic based Pharmacophore performed fairly well at distinguishing active from the inactive compounds and yielded a greater diversity of active molecules whereas the number of actives retrieved in the case of structure based screening was the highest.     

Synthesis of 2-(4-carboxybutenyl)- and 2-(4-carboxybutynyl)-cyclopentene-1-carboxamides

Syntheses of 2-(4-carboxybut-1-enyl/4-carboxypent-1-ynyl)cyclopentene-1-carboxamides, compounds designed to mimic the phosphoSer-Pro dipeptide motif (the recognition sequence for the prolyl cis-trans isomerase Pin1), have been developed. Stille, Sonogashira and Suzuki couplings were envisaged to join the pentynoic and pentenoic acid side chains to the 2-position of cyclopentene-1-carboxylate esters. The ring- and side-chain carboxylic acids required orthogonal protection for later attachment of a Ph-NH(4-nitrophenyl) unit to the cyclopentene-1-carbonyl. The cyclopentenecarboxylates were unmasked and standard PyBOP peptide coupling afforded the target compounds. Comparisons of two routes using Bu^t and Me esters are reported.     

The structural and electric properties of the perovskite system BaTiO3–Ba(Fe1/2Ta1/2)O3

Compounds in the pseudo-binary BaTiO₃–Ba(Fe_1/2Ta_1/2)O₃ system have been synthesized at 1500°C in air and characterized by X-ray and electron diffraction as well as impedance analysis and Mössbauer spectroscopy. The symmetry of Ba(Fe_1/2Ta_1/2)O₃ is found to be trigonal with the space group P3m1. Two solid solutions exist in the BaTi_1−xFe_x/1Ta_x/1O₃ system at room temperature. The first (SS1) is in the composition range 0⩽x⩽0.07 and is tetragonal, P4mm, while the second broader solid solution, (SS2) 0.12⩽x⩽1, is trigonal and has the space group P3m1. The conductivity becomes higher with reduced amount of Ti in the structure. The activation energy of conductivity differs between the two solid solutions, 0.80 eV for SS1 and 0.30 eV for SS2, which indicates different mechanisms. The maximum of the real part of the permittivity recorded for compounds in SS1 decreases towards room temperature with increasing amount of Fe/Ta doping and a high dielectric constant of around 7000 is found for BaTi_0.94Fe_0.03Ta_0.03O₃.     

Mechanism of antifeedant activity of plumbagin, a compound concerning the chemical defense in carnivorous plant

Dionaea muscipula Ellis accumulates a large amount of plumbagin (1), which operates as an antifeedant against predators. Content of 1 reached 0.5% weight of the fresh trap lobes. It was found that other carnivorous plants also accumulated similar naphthoquinone-type strong antifeedant. Thus, naphthoquinone analogs are widely used as an antifeedant among the carnivorous plants. By using several analogs of 1, we clarified that both the high volatility and high redox potential of 1 are important for its strong antifeedant activity. It was known that plumbagin stimulates the mitochondrial electron transport system as a result of intercepting electrons. These results suggested that the Droseraceae family possesses a universal defensive mechanism against predators, that is, accumulation of volatile naphthoquinone with high redox potential as defensive substance. Thus, it is estimated that highly volatile naphthoquinone of moderately high redox potential would be used as an antifeedant of weak toxicity.     

Structure Study of Bi2.5Na0.5Ta2O9 and Bi2.5Nam−1.5NbmO3m+3 (m=2-4) by Neutron Powder Diffraction and Electron Microscopy

The crystal structures of Bi_2.5Na_0.5Ta₂O₉ and Bi_2.5Na_m-1.5Nb_mO_3m+3 (m=3,4) have been investigated by the Rietveld analysis of their neutron powder diffraction patterns (λ=1.470 Å). These compounds belong to the Aurivillius phase family and are built up by (Bi₂O₂)²⁺ fluorite layers and (A_m-1B_mO_3m+1)^2- (m=2-4) pseudo-perovskite slabs. Bi_2.5Na_0.5Ta₂O₉ (m=2) and Bi_2.5Na_2.5Nb₄O₁₅ (m=4) crystallize in the orthorhombic space group A2₁am, Z=4, with lattice constants of a=5.4763(4), b=5.4478(4), c=24.9710 (15) and a=5.5095(5), b=5.4783(5), c=40.553(3) Å, respectively. Bi_2.5Na_1.5Nb₃O₁₂ (m=3) has been refined in the orthorhombic space group B2cb, Z=4, with the unit-cell parameters a=5.5024(7), b=5.4622(7), and c=32.735(4) Å. In comparison with its isostructural Nb analogue, the structure of Bi_2.5Na_0.5Ta₂O₉ is less distorted and bond valence sum calculations indicate that the Ta-O bonds are somewhat stronger than the Nb-O bonds. The cell parameters a and b increase with increasing m for the compounds Bi_2.5Na_m-1.5Nb_mO_3m+3 (m=2-4), causing a greater strain in the structure. Electron microscopy studies verify that the intergrowth of mixed perovskite layers, caused by stacking faults, also increases with increasing m.     

Heat capacity, enthalpy and entropy of ternary bismuth tantalum oxides

Heat capacity and enthalpy increments of ternary bismuth tantalum oxides Bi₄Ta₂O₁₁, Bi₇Ta₃O₁₈ and Bi₃TaO₇ were measured by the relaxation time method (2-280 K), DSC (265-353 K) and drop calorimetry (622-1322 K). Temperature dependencies of the molar heat capacity in the form C_pm=445.8+0.005451T−7.489×10⁶/T² J K⁻¹ mol⁻¹, C_pm=699.0+0.05276T−9.956×10⁶/T² J K⁻¹ mol⁻¹ and C_pm=251.6+0.06705T−3.237×10⁶/T² J K⁻¹ mol⁻¹ for Bi₃TaO₇, Bi₄Ta₂O₁₁ and for Bi₇Ta₃O₁₈, respectively, were derived by the least-squares method from the experimental data. The molar entropies at 298.15 K, S°_m(298.15 K)=449.6±2.3 J K⁻¹ mol⁻¹ for Bi₄Ta₂O₁₁, S°_m(298.15 K)=743.0±3.8 J K⁻¹ mol⁻¹ for Bi₇Ta₃O₁₈ and S°_m(298.15 K)=304.3±1.6 J K⁻¹ mol⁻¹ for Bi₃TaO₇, were evaluated from the low-temperature heat capacity measurements.     

Diazapolycyclic compounds—XIVTetrahedron33, 2109 (1977).: Epoxides from diazaquinone adducts: synthesis and stereochemical characterization

Epoxidation by m-chloroperbenzoic acid of adducts obtained by Diels-Alder reaction of pyridazine-1,4-dione, phthalazine-1,4-dione and benzo(g)phthalazine-1,4-dione with substituted 1,3-butadienes is reported. Although the epoxidation takes place in most of the cases in good yields, no reaction is observed in adducts which lack electron-donating groups attached to the double bond, and their epoxides must be obtained from the corresponding bromohydrines. The reaction affords either a single product or a mixture of cis and trans isomers, according to the location of the substituents in the piperidazine ring. The stereochemistry of these compounds is studied from their ¹H NMR spectra and by X-rays diffraction methods.