Novel β-dicarbonyl derivatives as inhibitors of aminopeptidase N (APN)

Most zinc metalloproteases are over-expressed in tumor cells and play a critical role in the genesis, development, and metastasis of tumors. Novel zinc binding groups (ZBGs) represent a novel strategy to obtain optimal potency and selectivity for zinc metalloproteases inhibitors. Here we described the design, synthesis, and biological studies of novel β-dicarbonyl derivatives as aminopeptidase N (APN/CD13) inhibitors. The results demonstrated that some compounds exhibited moderate to good inhibitory activities against APN with compound 5c being the most potent, suggesting that 5c could serve as new lead for the future APN inhibitor development. The results further confirm our design rationale of β-dicarbonyl moiety as a new ZBG, which may provide a new direction for the design and discovery of zinc metalloproteases inhibitors as new anti-tumor agents.     

Novel aminopeptidase N inhibitors derived from antineoplaston AS2–5 (Part II)

As our ongoing work, a series of peptidomimetic l-iso-glutamine derivatives derived from antineoplaston AS2–5 scaffold were prepared and their APN/CD13 and MMP-2 inhibitory activities were evaluated hereby. The results displayed that these compounds exhibited selective inhibition against APN as compared with MMP-2, with IC₅₀ values in micromole range. Compounds A1 and A2 showed comparable APN inhibitory activities than the positive control bestatin.     

Novel aminopeptidase N inhibitors derived from antineoplaston AS2–5 (Part I)

Overexpression of zinc-dependent metalloproteinase, aminopeptidase N (APN/CD13), is considered to be involved in the process of tumor invasion and metastasis. Herein we describe the synthesis and in vitro enzymatic inhibition assay of antineoplaston AS2–5 scaffold peptidomimetic compounds. The results demonstrated that most of these l-iso-glutamine derivatives displayed selective inhibitory activity against APN as compared with MMP-2, with IC₅₀ values in the micromole range. The structure–activity relationships were also briefly discussed.     

New aromatic monoesters of α-aminoaralkylphosphonic acids as inhibitors of aminopeptidase N/CD13

A series of new aromatic monoesters of α-aminoaralkylphosphonic acids were synthesized by selective hydrolysis of corresponding aromatic diesters of α-aminoaralkylphosphonic acids. New potential inhibitors of aminopeptidase N/CD13, an enzyme important in tumour angiogenesis, were developed. Some derivatives of the homophenylalanine and norleucine related monoaryl phosphonates displayed higher inhibition potency than corresponding α-aminoaralkylphosphonic acids toward aminopeptidase N/CD13. The effect of one of the new inhibitors on the growth of human PANC-1 and HT-1080 cell lines was examined, either alone or in combination with TNF-α.     

Novel macrocyclic HCV NS3 protease inhibitors derived from α-amino cyclic boronates

A novel series of P2–P4 macrocyclic HCV NS3/4A protease inhibitors with α-amino cyclic boronates as warheads at the P1 site was designed and synthesized. When compared to their linear analogs, these macrocyclic inhibitors exhibited a remarkable improvement in cell-based replicon activities, with compounds 9a and 9e reaching sub-micromolar potency in replicon assay. The SAR around α-amino cyclic boronates clearly established the influence of ring size, chirality and of the substitution pattern. Furthermore, X-ray structure of the co-crystal of inhibitor 9a and NS3 protease revealed that Ser-139 in the enzyme active site traps boron in the warhead region of 9a, thus establishing its mode of action.     

Novel non-peptide β-secretase inhibitors derived from structure-based virtual screening and bioassay

This Letter describes an efficient approach by integrating virtual screening with bioassay technology for finding small organic inhibitors targeting β-secretase (BACE-1). Fifteen hits with inhibitory potencies ranging from 2.8 to 118 μM (IC₅₀) against β-secretase were successfully identified. Compound 12 with IC₅₀ of 2.8 μM is the most potent hit against BACE-1. Docking simulation from gold 3.0 suggests putative binding mode of 12 in BACE-1 and potential key pharmacophore groups for further designing of non-peptide compounds as more powerful inhibitors against BACE-1.     

Novel Notch-sparing γ-secretase inhibitors derived from a peroxisome proliferator-activated receptor agonist library

Screening of our library of peroxisome proliferator-activated receptor (PPAR) agonists yielded several phenylpropanoic acid-derived γ-secretase inhibitors (GSIs). Structure–activity relationship studies indicated that (R)-configuration of α-substituted phenylpropanoic acid structure and cinnamic acid structure is favorable to prepare Notch-sparing GSIs.     

Novel PDE5 inhibitors derived from rutaecarpine for the treatment of Alzheimer’s disease

A series of novel rutaecarpine derivatives were synthesized and subjected to pharmacological evaluation as PDE5 inhibitors. The structure–activity relationships were discussed and their binding conformation and simultaneous interaction mode were further clarified by the molecular docking studies. Among the 25 analogues, compound 8i exhibited most potent PDE5 inhibition with IC₅₀ values about 0.086 μM. Moreover, it also produced good effects against scopolamine-induced cognitive impairment in vivo. These results might bring significant instruction for further development of potential PDE5 inhibitors derived from rutaecarpine as a good candidate drug for the treatment of Alzheimer’s disease.     

A binuclear copper(II) complex of the schiff base derived from 1,1′-(2,6-pyridyl)-bis-1,3-butanedione and 3-amino-1-propanol

The reaction of Cu(ClO₄)₂·6H₂O with the Schiff base derived from 1,1′-(2,6-pyridyl)-bis-1,3-butanedione and 3-amino-1-propanol, (H₄L²), yields the complex Cu(H₄L²)(ClO₄)₂·H₂O. The crystal structure of this complex is triclinic, R = 0.0521, 5602 reflections. The species is dimeric leading to a binuclear copper(II) complex in which the well- separated (8.93 Å intramolecular and 5.46 Å inter- molecular) copper(II) atoms are in distorted square pyramidal geometries.     

A new series of N2-substituted-5-(p-toluenesulfonylamino)phthalimide analogues as α-glucosidase inhibitors

Several members of a new family of non-sugar-type α-glycosidase inhibitors, bearing a 5-(p-toluenesulfonylamino)phthalimide moiety and various substituent at the N2 position, were synthesized and their activities were investigated. The newly synthesized compounds displayed different inhibition profile towards yeast α-glycosidase and rat intestinal α-glycosidase. Almost all the compounds had strong inhibitory activities against yeast α-glycosidase. Regarding rat intestinal α-glycosidase, only analogs with N2-aromatic substituents displayed varying degrees of inhibitory activities on rat intestinal maltase and lactase and nearly all compounds showed no inhibition against rat intestinal α-amylase. Structure–activity relationship studies indicated that 5-(p-toluenesulfonylamino)phthalimide moiety is a favorable scaffold to exert the α-glucosidase inhibitory activity and substituents at the N2 position have considerable influence on the efficacy of the inhibition activities.     

The mimics of Nε-acyl-lysine derived from cysteine as sirtuin inhibitors

Sirtuin inhibitors as physiological research tools and therapeutic potentials have caught many attentions in last decades. The mimics of acyl lysine have been approved to be a very efficient strategy for development of mechanism-based sirtuin inhibitors. In current study, a novel scaffold of l-S-(3-carboxamidopropyl) cysteine (l-CAPC) has been exploited for design and synthesis of sirtuin inhibitors. As a result, the mimics of N^ε-acyl-lysine derived from cysteine including small molecules (5a–m) and peptides (9a–m) have been synthesized. Among these, the peptides 9g and 9h were found to be the most inhibitory potency and selectivity against SIRT2.     

Syntheses and antitumor activities of N′1,N′3-dialkyl-N′1,N′3-di-(alkylcarbonothioyl) malonohydrazide: The discovery of elesclomol

A series of N′¹,N′³-dialkyl-N′¹,N′³-di(alkylcarbonothioyl) malonohydrazides have been designed and synthesized as anticancer agents by targeting oxidative stress and Hsp70 induction. Structure–activity relationship (SAR) studies lead to the discovery of STA-4783 (elesclomol), a novel small molecule that has been evaluated in a number of clinical trials as an anticancer agent in combination with Taxol.     

Preparation,properties and crystal structures of nickel(II) complexes with acyclic schiff bases derived from 2,6-diformyl-4-chlorophenol and 1,5-diamino-3-thiapentane or 3,3′-diamino-N-methyl-dipropylamine

Nickel(II) complexes with the compartmental Schiff bases derived from 2,6-diformyl-4-chlorophenol and 1,5-diamino-3-thiapentane (H₂L¹) or 3,3′-diamino-N-methyl-dipropylamine (H₂L²) were synthesized, and the crystal structures of [Ni(L¹)- (py)₂] and [Ni(L²)(dmf)]·H₂0 were determined by X-ray crystallography.Ni(L¹)(py)₂ is monoclinic, space group C2/c, with a= 18.457(6), b = 11.116(7), c= 16.098(6) Å, and β = 115.79(5)°; D_c = 1.49 g cm⁻³ for Z = 4. The structure was refined to the final R of 6.9%. The molecule has C₂ symmetry. The nickel atom is six-coordinated octahedral. Selected bond lengths are: NiO 2.04(1) Å, NiN (L¹) 2.08(1) Å, NiN(py) 2.17(1) Å.[Ni(L²)(dmf)]·H₂O is monoclinic, space group P2₁/n, with a = 17.329(6), b = 13.322(7), c = 12.476(7) Å and β = 95.43(5)°; D_c = 1.45 g cm⁻³ for Z = 4. The structure was refined to the final R of 5.1%. The nickel atom is bonded in the octahedral geometry to the bianionic pentadentate ligand L² and to one molecule of dimethylformamide. Selected bond lengths are: NiO (charged) 2.063(3) Å (mean value), NiO (neutral) 2.120(3) Å, NiN (planar) 2.050(3) Å (mean value), NiN (tetrahedral) 2.177(3) Å.     

Novel small renin inhibitors containing 4,5- or 3,5-dihydroxy-2-substituted-6-phenylhexanamide replacements at the P2P3 sites

Renin inhibitors containing a 4,5- or a 3,5-dihydroxy-2-substituted-6-phenylhexanamide fragment at the P₂---P₃ sites have been prepared and evaluated. The four possible diastereomeric diols of the two series of inhibitors were synthesized to determine the optimal configuration of the carbinol centers for these replacements. The most potent inhibitors of each series, 1a and 2c have a molecular weight of only 503 and IC₅₀ values of 23 and 20 nM in a human plasma renin assay at pH 6.0. Their very low aqueous solubility limited their further evaluation. The efficacy of these P₂---P₃ replacements is a result of their ability to maintain the important hydrogen-bonds with the enzyme. Due to conformational differences with the dipeptide, adjustment at the P₂ side chain was required. These 4,5- and 3,5-dihydroxyhexanamide segments could be seen as novel N-terminal dipeptide replacements.     

Solution-phase microwave assisted parallel synthesis,biological evaluation and in silico docking studies of N,N′-disubstituted thioureas derived from 3-chlorobenzoic acid

A facile and robust microwave-assisted solution phase parallel synthesis protocol was exercised for the development of a 38-member library of N,N′-disubstituted thiourea analogues (1–38) by using an identical set of conditions. The reaction time for synthesis of N,N′-disubstituted thiourea analogues was drastically reduced from a reported duration of 8–12 h for conventional methods to only 1.5–2.0 min. All the derivatives (1–38) were characterized by physico-analytical techniques such as elemental analysis in combination with FT-IR, ¹H, ¹³C NMR and by single crystal XRD analysis have also been performed. These compounds were screened for their in vitro urease inhibition activities. Majority of compounds exhibited potent urease inhibition activities, however, the most significant activity was found for 16, with an IC₅₀ value of 1.23 ± 0.1 μM. Furthermore, the synthesized compounds were screened for their cytotoxic potential against lungs cancer cell lines. Cell culture studies demonstrated significant toxicity of the compounds on the cell lines, and the levels of toxicity were altered in the presence of various side groups. The molecular docking studies of the most potent inhibitors were performed to identify the probable binding modes in the active site of the urease enzymes. These compounds have a great potential and significance for further investigations.     

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3′-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23 samples, which were each profiled by at least one of the four platform-tissue preparation combinations). Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR<0.01) on both the frozen tissue (∼9.6K genes) and FFPET (∼8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (∼4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.     

3-(3-Azido-2,3-Dideoxy-β-D-erythro pentofuranosyl)-thymine from 3′-Azido-3′-deoxythymidine (AZT). An Intriguing Rearrangement

Abstract

During the course of preparation of 3′-azido-3′-deoxythymidine (AZT), we observed consistent formation of an isomer of AZT (2-4%) which was isolated and the structure established as 3-(3-azido-2,3-dideoxy-β-D-ezythro pentofuranosyl)thymine. In a more detailed study, this rearrangement was found to occur during the treatment of 2,3′-anhydro-5′-O-tritylthymidine (1) with LiN₃ in aqueous DMF.     

NMR Studies of N 1- and N 3-(D-2′-Deoxyribofuranosyl) Nucleosides from Ethyl 5-Aminoimidazole-4-Carboxylate

Abstract

The conformation of deoxyribosides derived from N¹ and N³ substitution of the aglycone ethyl 5-aminoimidazole-4-carboxylate (AICE) has been determined by ¹H and ¹³C NMR spectroscopy. The deoxyribose ring shows considerable variation in the form and population of the contributing N and S conformers but the syn/anti ratio is similar to that in the purine analogues.     

Stereocontrolled Facile Synthesis and Biological Evaluation of (3′S) and (3′R)-3′-Amino (and Azido)-3′-Deoxy Pyranonucleosides

This article describes the synthesis of (3 ′S) and (3 ′R)-3 ′-amino-3 ′-deoxy pyranonucleosides and their precursors (3 ′S) and (3 ′R)-3 ′-azido-3 ′-deoxy pyranonucleosides. Azidation of 1,2:5,6-di-O-isopropylidene-3-O-toluenesulfonyl-α-D-allofuranose followed by hydrolysis and subsequent acetylation afforded 3-azido-3-deoxy-1,2,4,6-tetra-O-acetyl-D-glucopyranose, which upon coupling with the proper silylated bases, deacetylation, and catalytic hydrogenation, obtained the target 3 ′-amino-3 ′-deoxy-β-D-glucopyranonucleosides. The desired 1-(3 ′-amino-3 ′-deoxy-β-D-allopyranosyl)5-fluorouracil was readily prepared from the suitable imidazylate sugar after azidation followed by a protection/deprotection sequence and reduction of the unprotected azido precursor. No antiviral activity was observed for the novel nucleosides. Moderate cytostatic activity was recorded for the 5-fluorouracil derivatives.