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.     

De novo design and synthesis of a μ-conotoxin KIIIA peptidomimetic

μ-Conotoxin KIIIA blocks voltage-gated sodium channels and displays potent analgesic activity in mice models for pain. Structure–activity studies with KIIIA have shown that residues important for sodium channel activity are presented on an α-helix. Herein, we report the de novo design and synthesis of a three-residue (Lys7, Trp8, His12) peptidomimetic based on a novel diketopiperazine (DKP) carboxamide scaffold.     

De novo design of transmembrane helix–helix interactions and measurement of stability in a biological membrane

Membrane proteins regulate a large number of cellular functions, and have great potential as tools for manipulation of biological systems. Developing these tools requires a robust and quantitative understanding of membrane protein folding and interactions within the bilayer. With this in mind, we have designed a series of proteins to probe the net thermodynamic contribution of well-known sequence motifs to transmembrane helix-helix association in a biological membrane. The proteins were designed from first principles (de novo) using current knowledge about membrane insertion and stabilizing interaction motifs. A simple poly-Leu “scaffold” was decorated with individual helix interaction motifs (G-XXX-G, polar residues, heptad repeat) to create transmembrane helix–helix interactions of increasing strength. The GALLEX assay, an in vivo assay for measurement of transmembrane helix self-association, was combined with computational methods to characterize the relative strength and mode of interaction for each sequence. In addition, the apparent free energy contribution (ΔΔG^app) of each motif to transmembrane helix self-association was measured in a biological membrane, results that are the first of their kind for these de novo designed sequences, and suggest that the free energy barrier to overcoming weak association is quite small (< 1.4 kcal mol^− 1) in a natural membrane. By quantifying and rationalizing the contribution of key motifs to transmembrane helix association, our work offers a route to direct the design of novel sequences for use in biotechnology or synthetic biology (e.g. molecular switches) and to predict the effects of sequence modification in known transmembrane domains (for control of cellular processes).     

Increase in synthesis and stability of σ 32 on treatment with inhibitors of DNA gyrase in Escherichia coli

We report here that in Escherichia coli, the anti-bacterial agent nalidixic acid induces transient stabilization and increased synthesis of σ³², accompanied by the induction of heat shock proteins (Dnak and GroEL proteins). The induction of heat shock proteins, increased synthesis of σ³², and stabilization of σ³² observed on treatment of wild-type cells with nalidixic acid were not observed in a nalA26 mutant, a strain that is resistant to nalidixic acid as the result of a mutation in the gyrA gene. Not only oxolinic acid, but also novobiocin, whose targets are the A and B subunits of DNA gyrase, respectively, also induced stabilization and increased synthesis of σ³². Thus, inhibition of the activity of DNA gyrase may cause stabilization and increased synthesis of σ³², resulting in turn in induction of heat shock proteins.     

Protein–ligand interaction-guided discovery of novel VEGFR-2 inhibitors

Abstract

As an effective target in abnormal angiogenesis-related tumor treatment, VEGFR-2 has small-molecule inhibitors of various scaffolds being approved for treating diseases such as renal carcinoma, non-small cell lung cancer, etc. However, endogenous and acquired drug resistance are still considered to be the main contributors for the failure of VEGFR-2 clinical candidates. Therefore, development of novel VEGFR-2 inhibitors is still urgently needed in the market but also challenging. In this work, residues including Asp1046, Ile1025, HIS1026, Cys919 and Lys868 were identified as the most important residues for Hbonded interaction, while His1026, Asp1046, Glu885, Ile1025 and Leu840 exhibited critical role for the nonbonded interactions through a comprehensive analysis of protein–ligand interactions, which plays critical roles in the binding of compounds and targets. Guided by the analysis of binding interactions, a total of 10 novel VEGFR-2 inhibitors based on N-methyl-4-oxo-N-propyl-1,4-dihydroquinoline-2-carboxamide scaffold were discovered through fragment-based drug design and structure-based virtual screening, which expands the chemical space of current VEGFR-2 inhibitors. Biological activity evaluation showed that even though the enzymatic activity of these compounds against VEGFR-2 were inferior to that of the positive controls sorafenib and motesanib, compound I-10 showed moderate HepG2 cell inhibitory activity with an IC₅₀ value of 33.65?μM and eight compounds exhibited moderate or higher HUVEC inhibitory activity in the range of 19.54–57.98?μM compared to the controls. Particularly, the HUVEC inhibitory activity of compound I-6 (IC₅₀ = 19.54?μM) outperformed motesanib and can be used as starting points for further optimization and development for cancer treatment.

Communicated by Ramaswamy H. Sarma     

Discovery of novel Jak2–Stat pathway inhibitors with extended residence time on target

The discovery of the activating mutation V617F in the JH2 domain of Jak2 and the modulation of oncogenic Stat3 by Jak2 inhibitors have spurred a great interest in the inhibition of the Jak2/Stat pathway in oncology. In this Letter, we communicate the discovery of novel inhibitors of the Jak2/Stat5 axis, the N-(1H-pyrazol-3-yl)pyrimidin-2-amino derivatives. The rationale, synthesis and biological evaluation of these derivatives are reported. Two lead analogs from this series, 6 and 9, displayed prolonged residence time on Jak2, at enzymatic level. Although 6 and 9 exhibited moderate selectivity in a selected kinase panel, we chose to test these inhibitors in vivo as a consequence to their long residence time. However, extended inhibition of Jak2 due to the long residence time, in the form of inhibiting phosphorylation of downstream Stat5, was not recapitulated in an in vivo setting.     

Confirmation of quinolone-induced formation of gyrase–DNA conjugates using AFM

It was demonstrated in our studies that norfloxacin, a representative member of quinolone antibiotics, can indeed stabilize the gyrase–DNA complex formed during enzymatic cycle. In addition, the formation of the drug-induced complex has been firstly visualized through our atomic force microscopic examination.     

Identification of novel triazole inhibitors of Wnt/β-catenin signaling based on the Niclosamide chemotype

Dysregulation of the Wnt signaling pathway is an underlying mechanism in multiple diseases, particularly in cancer. Until recently, identifying agents that target this pathway has been difficult and as a result, no approved drugs exist that specifically target this pathway. We reported previously that the anthelmintic drug Niclosamide inhibits the Wnt/β-catenin signaling pathway and suppresses colorectal cancer cell growth in vitro and in vivo. In an effort to build on this finding, we sought to discover new Wnt/β-catenin inhibitors that expanded the chemotype structural diversity. Here, we asked a specific SAR question unresolved in previous SAR studies of Niclosamide’s inhibition of Wnt/β-catenin signaling to identify a new structural class of Wnt/β-catenin signaling inhibitors based on a triazole motif. Similar to Niclosamide, we found that the new triazole derivatives internalized Frizzled-1 GFP receptors, inhibited Wnt/β-catenin signaling in the TOPflash assay and reduced Wnt/β-catenin target gene levels in CRC cells harboring mutations in the Wnt pathway. Moreover, in pilot SAR studies, we found the Wnt/β-catenin SAR trends in the anilide region were generally similar between the two chemical classes of inhibitors. Overall, these studies demonstrate the ability to use the SAR of the Niclosamide salicylanilide chemical class to expand the structural diversity of Wnt/β-catenin inhibitors.     

De novo design of α,β-didehydrophenylalanine containing peptides: from models to applications

The de novo design of peptides and proteins has emerged as an approach for investigating protein structure and function. The success relies heavily on the ability to design relatively short peptides that can adopt stable secondary structures. To this end, substitution with α,β-dehydroamino acids, especially α,β-didehydrophenylalanine (ΔPhe or ΔF) has blossomed in manifold directions, providing a rich diversity of well-defined structural motifs. Introduction of α,β-didehydrophenylalanine induces β-bends in small and 3(10)-helices in longer peptide sequences. Most favorable conformation of ΔF residues are (φ,ψ) ～(60°, 30°), (-60°, -30°), (-60°, 150°), and (60°, -150°). These features have been exploited in designing helix-turn-helix, helical bundle arrangements, and glycine zipper type super secondary structural motifs. The unusual capability of α,β-didehydrophenylalanine ring to form a variety of multicentered interactions (N-H…O, C-H…O, C-H…π, and N-H…π) suggests its possible exploitation for future de novo design of supramolecular structures. This work has now been extended to the de novo design of peptides with antibiotic, antifibrillization activity, etc. More recently, self-assembling properties of small dehydropeptides have been explored. This review focuses primarily on the structural and functional behavior of α,β-didehydrophenylalanine containing peptides.     

Quantitative structure–activity relationship analysis using deep learning based on a novel molecular image input technique

Quantitative structure–activity relationship (QSAR) analysis uses structural, quantum chemical, and physicochemical features calculated from molecular geometry as explanatory variables predicting physiological activity. Recently, deep learning based on advanced artificial neural networks has demonstrated excellent performance in the discipline of QSAR research. While it has properties of feature representation learning that directly calculate feature values from molecular structure, the use of this potential function is limited in QSAR modeling. The present study applied this function of feature representation learning to QSAR analysis by incorporating 360° images of molecular conformations into deep learning. Accordingly, I successfully constructed a highly versatile identification model for chemical compounds that induce mitochondrial membrane potential disruption with the external validation area under the receiver operating characteristic curve of ≥0.9.     

Toward the rational design of molecular rotors ion sensors based on α,γ-cyclic peptide dimers

A dimer-forming self-assembling cyclic hexapeptide with a control register and a large association constant in water is described. The self-assembly process is followed by pyrene-excimer emission and the main diastereomeric dimer present in solution is switched by controlled addition of divalent cations (e.g., Ca, Mg) or oxalic acid.     

Structure–Activity Relationship of novel phenylacetic CXCR1 inhibitors

We reported recently the Structure–Activity Relationship (SAR) of a class of CXCL8 allosteric modulators. They invariably share a 2-arylpropionic moiety so far considered a key structural determinant of the biological activity. We show the results of recent SAR studies on a novel series of phenylacetic derivatives supported by a combined approach of mutagenesis experiments and conformational analysis. The results suggest novel insights on the fine role of the propionic/acetic chain in the modulation of CXCL8 receptors.     

Structure and property based design, synthesis and biological evaluation of γ-lactam based HDAC inhibitors

Histone deacetylases (HDACs) are involved in post-translational modification and gene expression. Cancer cells recruited amounts of HDACs for their survival by epi-genetic down regulation of tumor suppressor genes. HDACs have been the promising targets for treatment of cancer, and many HDAC inhibitors have been investigated nowadays. In previous study, we synthesized δ-lactam core HDAC inhibitors which showed potent HDAC inhibitory activities as well as cancer cell growth inhibitory activities. Through QSAR study of the δ-lactam based inhibitors, the smaller core is suggested as more active than larger one because it fits better in narrow hydrophobic tunnel of the active pocket of HDAC enzyme. The smaller γ-lactam core HDAC inhibitors were designed and synthesized for biological and property optimization. Phenyl, naphthyl and thiophenyl groups were introduced as the cap groups. Hydrophobic and bulky cap groups increase potency of HDAC inhibition because of hydrophobic interaction between HDAC and inhibitors. In overall, γ-lactam based HDAC inhibitors showed more potent than δ-lactam analogues.     

Discovery of 1-arylpyrrolidone derivatives as potent p53–MDM2 inhibitors based on molecule fusing strategy

Introducing an aryl moiety to our previous pyrrolidone scaffold by molecule fusing strategy afforded two sets of isopropylether–pyrrolidone and α-phenylethylamine–pyrrolidone derivatives. Two novel compounds 8b and 8g of the latter serial showed potent p53–MDM2 inhibitory activities with K_i values of 90 nM which were three-time higher than that of the parent compound. We also confirmed compound 8b can activate p53 proteins in lung cancer A549 cells. The results offered us valuable information for further lead optimization.     

Discovery of novel fragments inhibiting O-acetylserine sulphhydrylase by combining scaffold hopping and ligand–based drug design

Several bacteria rely on the reductive sulphur assimilation pathway, absent in mammals, to synthesise cysteine. Reduction of virulence and decrease in antibiotic resistance have already been associated with mutations on the genes that codify cysteine biosynthetic enzymes. Therefore, inhibition of cysteine biosynthesis has emerged as a promising strategy to find new potential agents for the treatment of bacterial infection. Following our previous efforts to explore OASS inhibition and to expand and diversify our library, a scaffold hopping approach was carried out, with the aim of identifying a novel fragment for further development. This novel chemical tool, endowed with favourable pharmacological characteristics, was successfully developed, and a preliminary Structure–Activity Relationship investigation was carried out.     

Hot spot-based design of small-molecule inhibitors for protein–protein interactions

Protein–protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined.     

Synthesis and evaluation of novel orally active p53–MDM2 interaction inhibitors

We have discovered and reported potent p53–MDM2 interaction inhibitors possessing dihydroimidazothiazole scaffold. Our lead showed strong activity in vitro, but did not exhibit antitumor efficacy in vivo for the low metabolic stability. In order to obtain orally active compounds, we executed further optimization of our lead by the improvement of physicochemical properties. Thus we furnished optimal compounds by introducing an alkyl group onto the pyrrolidine at the C-2 substituent to prevent the metabolism; and modifying the terminal substituent of the proline motif improved solubility. These optimal compounds exhibited good PK profiles and significant antitumor efficacy with oral administration on a xenograft model using MV4-11 cells having wild type p53.     

A combined molecular modeling study on a series of pyrazole/isoxazole based human Hsp90α inhibitors

Inhibition of the protein chaperone Hsp90α is a promising approach for cancer therapy. In this work, a molecular modeling study combining pharmacophore model, molecular docking and three-dimensional quantitative structure-activity relationships (3D-QSAR) was performed to investigate a series of pyrazole/isoxazole scaffold inhibitors of human Hsp90α. The pharmacophore model can provide the essential features required for the biological activities of the inhibitors. The molecular docking study can give insight into the binding mode between Hsp90α and its inhibitors. 3D-QSAR based on CoMFA and CoMSIA models were performed from three different strategies for conformational selection and alignment. The receptor-based models gave the most statistically significant results with cross-validated q ² values of 0.782 and 0.829 and r ² values of 0.909 and 0.968, for CoMFA and CoMSIA respectively. Furthermore, the 3D contour maps superimposed within the binding site of Hsp90α could help to understand the pivotal interaction and the structural requirements for potent Hsp90α inhibitors. The results show 4-position of pyrazole/isoxazole ring requires bulky and hydrophobic groups, and bulky and electron repulsion substituent of 5-amides is favorable for enhancing activity. This study will be helpful for the rational design of new potent Hsp90α inhibitors.