Identification and structure–activity relationship of purine derivatives as novel MTH1 inhibitors

The human mutT homolog‐1 (MTH1) protein prevents the incorporation of oxidized nucleotides such as 2‐OH‐dATP and 8‐oxo‐dGTP during DNA replication by hydrolyzing them into their corresponding monophosphates. It was found previously that cancer cells could tolerate oxidative stress due to this enzymatic activity of MTH1 and its inhibition could be a promising approach to treat several types of cancer. This finding has been challenged recently with increasing line of evidence suggesting that the cancer cell‐killing effects of MTH1 inhibitors may be related to their engagement of off‐targets. We have previously reported a few purine‐based MTH1 inhibitors that enabled us to elucidate the dispensability of MTH1 in cancer cell survival. Here, we provide a detailed process of the identification of purine‐based MTH1 inhibitors. Several new compounds with potency in the submicromolar range are disclosed. Furthermore, the structure–activity relationship and associated binding mode prediction using molecular docking have provided insights for the development of highly potent MTH1 inhibitors.     

3D‐QSAR,molecular docking,and ONIOM studies on the structure–activity relationships and action mechanism of nitrogen‐containing bisphosphonates

Nitrogen‐containing bisphosphonates (N‐BPs) have been used widely to treat various bone diseases by inhibiting the key enzyme farnesyl pyrophosphate synthase (FPPS) in the mevalonate pathway. Understanding the structure–activity relationships and the action mechanisms of these bisphosphonates is instructive for the design and the development of novel potent inhibitors. Here, a series of N‐BPs inhibitors of human FPPS (hFPPS) were investigated using a combination of three‐dimensional quantitative structure–activity relationship (3D‐QSAR), molecular docking, and three‐layer ONIOM studies. The constructed 3D‐QSAR model yielded a good correlation between the predicted and experimental activities. Based on the analysis of comparative molecular field analysis (CoMFA) contour maps, a series of novel N‐BPs inhibitors were designed and ten novel potent N‐BPs inhibitor candidates were screened out. Molecular docking and ONIOM (B3LYP/6‐31 + G*:PM6:Amber) calculations revealed that the inhibitors bound to the active site of hFPPS via hydrogen‐bonding interactions, hydrophobic interactions, and cation‐π interactions. Six novel N‐BPs inhibitors with better biological activities and higher lipophilicity were further screened out from ten candidates based on the calculated interaction energy. This study will facilitate the discovery of novel N‐BPs inhibitors with higher activity and selectivity.     

Discovery and structure–activity relationship of plastoquinone analogs as anticancer agents against chronic myelogenous leukemia cells

Two series of amino‐1,4‐benzoquinones ( AQ1–18 ) based on the structural analogs of plastoquinones were synthesized and the structure–activity relationship against chronic myelogenous leukemia activity was examined. All of the synthesized compounds were tested for their cytotoxic effects on different leukemic cell lines. Of interest, AQ15 exhibited a better selectivity than the reference drug imatinib on cancer cells. Owing to this, AQ15 was selected for a further apoptosis/necrosis evaluation where AQ15 ‐treated K562 cells demonstrated similar apoptotic effects like imatinib‐treated cells at their IC₅₀ values. The inhibitory effects of AQ15 and the other three compounds with various activities against eight tyrosine kinases, including ABL1, were investigated. AQ15 showed weak activity against ABL1, and a correlation was observed between the anti‐K562 and anti‐ABL1 activities. The binding mode of AQ15 into the ATP binding pocket of ABL1 kinase was predicted in silico, showing the formation of some key interactions. In addition, AQ15 was shown to suppress the downstream signaling of BCR‐ABL in K562 cells. Finally, AQ15 obviously cleaved DNA in the presence of an iron(II) complex system, indicating that this can be the major mechanism of its antiproliferative action, whereas the mild inhibition of ABL kinase is just in‐part mechanism of its overall outstanding cellular activity.     

基于分子对接、定量构效关系和分子动力学研究筛选小分子SIRT1抑制剂

为了寻找和发现靶向SIRT1的治疗AML的新型先导化合物,本研究利用分子对接与MM-GBSA结合自由能计算进行虚拟筛选,从231 511个天然小分子类药分子库中筛选出8个潜在的SIRT1抑制剂,通过对已有的SIRT1抑制剂分子作为训练集和测试集进行QSAR建模,对筛选出的潜在SIRT1抑制剂分子进行活性预测,随后进行分...     

3D-QSAR and molecular docking studies on substituted isothiazole analogs as inhibitors against MEK-1 kinase

MEK-1 and MEK-2 are dual-specificity kinases and important components in the mitogen-activated protein kinase pathway. These enzymes are crucial for normal cell survival and are also expressed in several types of cancers, making them important targets for drug design. We have applied an integrated in silico approach that combines comparative molecular field analysis, comparative molecular similarity indices analysis, and molecular docking to study the structural determinants for the recognition of substituted isothiazole analogs as allosteric inhibitors against MEK-1 kinase. The best 3D-QSAR models for comparative molecular field analysis and comparative molecular similarity indices analysis were selected based on statistical parameters. 3D contour maps suggested that bulky or long-chain substitutions at the X position on the core part decrease the inhibitory activity, and the presence of a hydrogen bond donor substitution enhances the activity. The bulky and electronegative substitutions at the Y position on the core part enhance the activity of the inhibitors. Molecular docking studies reveal a large and hydrophobic pocket that accommodates the Y substitution and a polar pocket that accommodates substitutions on the X position and forms hydrogen bonding interactions with MEK-1 kinase. The results of the 3D-QSAR analysis corroborate with the molecular docking results, and our findings will serve as a basis for further development of better allosteric inhibitors of MEK-1 kinase against several cancers.     

In vivo structure–activity studies on the dark‐color‐inducing neurohormone of locusts

Abstract: In the 11‐residue long dark‐color‐inducing neurohormone (DCIN = [His⁷]‐corazonin), of locusts, from residue 2 to residue 11, one amino acid at each time was substituted by d ‐phenylalanine (d ‐Phe). The dark‐color‐inducing effect of these peptides was investigated in comparison with unaltered DCIN by a bioassay based on nymphs of a DCIN‐deficient albino mutant of the migratory locust, Locusta migratoria. Substitution of any single amino acid by d ‐Phe always reduced the activity, but did not abolish it completely. Maximum inactivation was obtained after substitution of Gln4, Ser6, or Trp9. The latter two residues are within the partial sequence ‐Ser‐Xxx‐Gly‐Trp‐ (Xxx = His in the DCIN) that seems to be important for the dark‐color‐inducing activity, as found also in another study (Insect Biochem. Mol. Biol. 32, 2002, 909). Gln4, however, is outside of this partial sequence. Minimal, although still considerable, inactivation occurred after substitution of Gly8, Phe3, or Asn11, despite the fact that Gly8 is within the ‐Ser‐Xxx‐Gly‐Trp‐ partial sequence. In conclusion, no single active core was found, indicating that the whole sequence of the DCIN is necessary to induce maximum darkening effect. No difference was found in the activity of the peptides in which Gly8 was substituted by d ‐Phe or by l ‐Phe. Therefore the ‐Ser‐Xxx‐Gly‐Trp‐ partial sequence does not seem to be stabilized by a type II β‐turn. Nevertheless, existence of another kind of turn that includes this partial sequence is feasible. A single unsuccessful attempt was made to discover an antagonist to the DCIN.     

In vivo structure–activity studies on the dark‐color‐inducing neurohormone of locusts

In the 11‐residue long dark‐color‐inducing neurohormone (DCIN = [His⁷]‐corazonin), of locusts, from residue 2 to residue 11, one amino acid at each time was substituted by d ‐phenylalanine (d ‐Phe). The dark‐color‐inducing effect of these peptides was investigated in comparison with unaltered DCIN by a bioassay based on nymphs of a DCIN‐deficient albino mutant of the migratory locust, Locusta migratoria. Substitution of any single amino acid by d ‐Phe always reduced the activity, but did not abolish it completely. Maximum inactivation was obtained after substitution of Gln4, Ser6, or Trp9. The latter two residues are within the partial sequence ‐Ser‐Xxx‐Gly‐Trp‐ (Xxx = His in the DCIN) that seems to be important for the dark‐color‐inducing activity, as found also in another study (Insect Biochem. Mol. Biol. 32, 2002, 909). Gln4, however, is outside of this partial sequence. Minimal, although still considerable, inactivation occurred after substitution of Gly8, Phe3, or Asn11, despite the fact that Gly8 is within the ‐Ser‐Xxx‐Gly‐Trp‐ partial sequence. In conclusion, no single active core was found, indicating that the whole sequence of the DCIN is necessary to induce maximum darkening effect. No difference was found in the activity of the peptides in which Gly8 was substituted by d ‐Phe or by L ‐Phe. Therefore the ‐Ser‐Xxx‐Gly‐Trp‐ partial sequence does not seem to be stabilized by a type II β‐turn. Nevertheless, existence of another kind of turn that includes this partial sequence is feasible. A single unsuccessful attempt was made to discover an antagonist to the DCIN.     

Synthesis,Evaluation of Pharmacological Activities and Quantitative Structure–Activity Relationship Studies of a Novel Group of bis(4‐Nitroaryl‐1,4‐dihyropyridine)

Voltage‐dependent calcium channels are crucial targets for a wide range of clinically active pharmacological agents. From these agents, 1,4‐dihydropyridines constitute a group of small organic compounds are based on a core pyridine structure which can both block and enhance calcium currents. They are considered specific for L‐Type calcium channels; however, other channel types, and in particular certain T‐Type channels, may show sensitivity to dihydropyridine compounds. In this study, we synthesized a novel group of bis‐1,4‐dihydropyridines using the procedure reported by Dagnino that involved the condensation of n‐alkyl diacetoacetate (n = 2–7) with methyl‐3‐aminocrotonate and nitrophenylaldehyde. The synthesis was run under two conditions: (i) reflux and (ii) microwave. Calcium channels antagonist activity were determined in vitro using guinea‐pig ileum longitudinal smooth muscle assay. Synthesis of these compounds was confirmed with 1H‐NMR, IR and mass spectrometry. Then IC₅₀ of them are calculated and compared with Nifedipine. Finally, the result of this pharmacological assay was used in quantitative structure–activity relationship studies utilizing multiple linear regression analysis. Most of these compounds are less active compared with Nifedipine. Decrease in activity is the result of increase in steric hindrance. The quantitative structure–activity relationship study indicates that the activity is related to the electrostatic and topological parameters and the distance between two C5‐esteric groups of 1,4‐dihydropyridine rings.     

Plant‐Derived Flavones as Inhibitors of Aurora B Kinase and Their Quantitative Structure–Activity Relationships

Although several plant‐derived flavones inhibit aurora B kinase (aurB), quantitative relationships between the structural properties of plant‐derived flavones and their inhibitory effects on aurB remain unclear. In this report, these quantitative structure–activity relationships were obtained. For quercetagetin, found in the Eriocaulon species, showing the best IC₅₀ value among the flavone derivatives tested in this report, further biological tests were performed using cell‐based assays, including Western blot analysis, flow cytometry, and immunofluorescence microscopy. In vitro cellular experiments demonstrated that quercetagetin inhibits aurB. The molecular‐binding mode between quercetagetin and aurB was elucidated using in silico docking. Quercetagetin binds to aurB, aurA, and aurC and prevents the active phosphorylation of all three aurora kinases. In addition, quercetagetin triggers mitotic arrest and caspase‐mediated apoptosis. These observations suggest that quercetagetin is an aurora kinase inhibitor. Induction of mitosis‐associated tumor cell death by quercetagetin is a promising strategy for developing novel chemotherapeutic anticancer agents.     

Quantitative structure–activity relationship (QSAR) study of elastase substrates and inhibitors

One hundred Suc-X-Y-Ala-pNA peptides (SUC: succinyl, pNA: p-nitroanilide, X, Y: Gly, Ala, Val, Leu, Ile, Phe, Pro, x-aminobutyric acid, norvaline, norleucine) were synthesized and their reaction constants with porcine pancreatic elastase (K_m, K_cat and K_cat/K_m) were determined. These reaction constants were quantitatively analyzed using the Free–Wilson/Fujita–Ban method. The contribution of amino acid side chains to the reaction constants K_m, K_cat and K_cat/K_m), expressed logarithmically, was found to be additive. On the other hand, 19 elastase inhibitors of the general formula CF₃CO-X-Y-Ala-pNA (X,Y: ten amino acids) were synthesized, and their inhibition constants were compared with the Michaelis constant for the corresponding substrates and analyzed using free-energy-related substituent constants. In the analysis of amino acid side chains in the Y position, the K_i value of the inhibitor was generally correlated to the K_m value of the substrate, which corresponded to the inhibitor, thus confirming the validity of the equation This study may serve as a prototypical approach to unraveling structure–activity relationships of peptide substrates and inhibitors of medicinal or agricultural importance.     

Quantitative structure–activity relationship studies of cyclooxygenase inhibitors: a comprehensive analysis

A quantitative structure‐activity relationship (QSAR) analysis of 10 structurally diverse set of compounds recently reported as cyclooxygenase (COX) inhibitors has been performed using ClogP, CMR, aromatic substituent constants, and suitable indicator variables. These revealed several important physicochemical and structural requirements for COX‐1, COX‐2 inhibitory activity, and selective inhibition of COX‐2 versus COX‐1 among these novel ligands. Seventeen QSAR models reported herein provide interesting insights in understanding the hydrophobic, steric, electronic, and structural requirements of COX inhibition among these individual set of compounds. These results may be used to further the design and development of selective COX‐2 inhibitors among these newly reported COX inhibitors. Drug Dev Res 64:220–231, 2005. © 2005 Wiley‐Liss, Inc.     

Design,microwave‐assisted synthesis,biological evaluation and molecular modeling studies of 4‐phenylthiazoles as potent fatty acid amide hydrolase inhibitors

Endocannabinoids, anandamide (AEA) and 2‐arachidonoylglycerol (2‐AG), are endogenous lipids that activate cannabinoid receptors. Activation of these receptors produces anti‐inflammatory and analgesic effects. Fatty acid amide hydrolase (FAAH) is a membrane enzyme that hydrolases endocannabinoids; thus, inhibition of FAAH represents an attractive approach to develop new therapeutics for treating inflammation and pain. Previously, potent rat FAAH inhibitors containing 2‐naphthyl‐ and 4‐phenylthiazole scaffolds were identified, but up to the present time, very little structure–activity relationship studies have been performed on these moieties. We designed and synthesized several analogs containing these structural motifs and evaluated their inhibition potencies against human FAAH enzyme. In addition, we built and validated a homology model of human FAAH enzyme and performed docking experiments. We identified several inhibitors in the low nanomolar range and calculated their ADME predicted values. These FAAH inhibitors represent promising drug candidates for future preclinical in vivo studies.