Alkaloidal sugar mimetics: biological activities and therapeutic applications

Alkaloids mimicking the structures of sugars inhibit glycosidases because of a structural resemblance to the sugar moiety of the natural substrate. Glycosidases are involved in a wide range of important biological processes, such as intestinal digestion, post-translational processing of glycoproteins and the lysosomal catabolism of glycoconjugates. The realization that alkaloidal sugar mimics might have enormous therapeutic potential in many diseases such as viral infection, cancer and diabetes led to increasing interest and demand for these compounds. In this review, the structural basis of the specificity of alkaloidal sugar mimics and their current and potential applications to biomedical problems are reviewed.     

Corosolic acid and its structural analogs: A systematic review of their biological activities and underlying mechanism of action

BackgroundThe corosolic acid (CA), also known as plant insulin, is a pentacyclic triterpenoid extracted from plants such as Lagerstroemia speciosa. It has been shown to have anti-diabetic, anti-inflammatory and anti-tumor effects. Its structural analogs ursolic acid (UA), oleanolic acid (OA), maslinic acid (MA), asiatic acid (AA) and betulinic acid (BA) display similar individual pharmacological activities to those of CA. However, there is no systematic review documenting pharmacological activities of CA and its structural analogues. This study aims to fill this gap in literature.PurposeThis systematic review aims to summarize the medical applications of CA and its analogues.MethodsA systematic review summarizes and compares the extraction techniques, pharmacokinetic parameters, and pharmacological effects of CA and its structural analogs. Hypoglycemic effect is one of the key inclusion criteria for searching Web of Science, PubMed, Embase and Cochrane databases up to October 2020 without language restrictions. ‘corosolic acid’, ‘ursolic acid’, ‘oleanolic acid’, ‘maslinic acid’, ‘asiatic acid’, ‘betulinic acid’, ‘extraction’, ‘pharmacokinetic’, ‘pharmacological’ were used to extract relevant literature. The PRISMA guidelines were followed.ResultsAt the end of the searching process, 140 articles were selected for the systematic review. Information of CA and five of its structural analogs including UA, OA, MA, AA and BA were included in this review. CA and its structural analogs are pentacyclic triterpenes extracted from plants and they have low solubilities in water due to their rigid scaffold and hydrophobic properties. The introduction of water-soluble groups such as sugar or amino groups could increase the solubility of CA and its structural analogs. Their biological activities and underlying mechanism of action are reviewed and compared.ConclusionCA and its structural analogs UA, OA, MA, AA and BA are demonstrated to show activities in lowering blood sugar, anti-inflammation and anti-tumor. Their oral absorption and bioavailability can be improved through structural modification and formulation design. CA and its structural analogs are promising natural product-based lead compounds for further development and mechanistic studies.     

Synthesis and Application of Negatively Charged PNA Analogues

Negatively charged DNA mimics containing phosphonate analogues of peptide nucleic acids were designed, and their physicochemical and biological properties were evaluated in the comparison with natural oligonucleotides, classical peptide nucleic acids, and morpholino phosphorodiamidate oligonucleotide analogues. The results obtained revealed a high potential of phosphonate-containing PNA derivatives for a number of biological applications, such as diagnostic, nucleic acids analysis, and inhibition of gene expression.     

The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability

Background and AimsPlant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes.MethodsWe identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization.Key resultsAll 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes – mechanisms that likely caused Cassandra’s subfamily formation and diversification.ConclusionsWe traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.     

Therapeutic potential of indole alkaloids in respiratory diseases: A comprehensive review

BackgroundIndole alkaloids are very promising for potential therapeutic purposes and appear to be particularly effective against respiratory diseases. Several experimental studies have been performed, both in vivo and in vitro, to evaluate the effectiveness of indole alkaloids for the management of respiratory disorders, including asthma, emphysema, tuberculosis, cancer, and pulmonary fibrosis.PurposeThe fundamental objective of this review was to summarize the in-depth therapeutic potential of indole alkaloids against various respiratory disorders.Study designIn addition to describing the therapeutic potential, this review also evaluates the toxicity of these alkaloids, which have been utilized for therapeutic benefits but have demonstrated toxic consequences. Some indole alkaloids, including scholaricine, 19-epischolaricine, vallesamine, and picrinine, which are derived from the plant Alstonia scholaris, have shown toxic effects in non-rodent models.MethodsThis review also discusses clinical studies exploring the therapeutic efficacy of indole alkaloids, which have confirmed the promising benefits observed in vivo and in vitro.ResultsThe indole alkaloidal compounds have shown efficacy in subjects with respiratory diseases.ConclusionThe available data established both preclinical and clinical studies confirm the potential of indole alkaloids to treat the respiratory disorders.     

Phosphono Peptide Nucleic Acids with a Constrained Hydroxyproline-Based Backbone

Abstract

DNA mimics representing negatively charged analogues of peptide nucleic acids (PNAs), particularly hetero-oligomers constructed from alternating phosphono-PNA residues (pPNA) and monomers on the base of trans-4-hydroxy-L-proline (HypNA) as well as mimics composed of phosphono-HypNA monomers (pHypNA) were tested in a set of in vitro and in vivo assays, and they demonstrated a high potential for the use in nucleic acid based diagnostic, isolation of nucleic acids and antisense experiments.     

Urease and Serine Protease inhibitory alkaloids from Isatis tinctoria

Phytochemical investigations on the alkaloidal fraction of the whole plant of the Isatis tinctoria led to the isolation of the alkaloids 1-6., 3′-Hydroxyepiglucoisatisin (3), Epiglucoisatisin (2) were found to be potent urease inhibitors in a concentration-dependent manner with IC₅₀ values 25.63 ± 0.74, 37.01 ± 0.41 and 31.72 ± 0.93, 47.33 ± 0.31 μM against Bacillus pasteurii & Jack bean urease, respectively. Compounds 3 and 2 also showed potent inhibitory potential against α-chymotrypsin with IC₅₀ values of 23.40 ± 0.21 and 27.45 ± 0.23 μM, respectively.     

Synthesis and Anti-HIV Activity of β-D-3′-Azido-2′,3′-unsaturated Nucleosides and β-D-3′-Azido-3′-deoxyribofuranosylnucleosides

Since the discovery of 3′-azido-3′-deoxythymidine (AZT) and 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) as potent and selective inhibitors of the replication of human immunodeficiency virus (HIV), there has been a growing interest for the synthesis of 2′,3′-didehydro-2′,3′-dideoxynucleosides with electron withdrawing groups on the sugar moiety. Here we described an efficient method for the synthesis of such nucleoside analogs bearing structural features of both AZT and d4T. The key intermediate, 3-azido-1,2-bis-O-acetyl-5-O-benzoyl-3-deoxy-D-ribofuranose, 5 was synthesized from commercially available D-xylose in five steps, from which a series of pyrimidine and purine nucleosides were synthesized in high yields. The resultant protected nucleosides were converted to target nucleosides using appropriate chemical modifications. The final nucleosides were evaluated as potential anti-HIV agents.     

Program MULDER -- a tool for extracting torsion angles from NMR data

MULDER (Mostly UniversaL Dihedral angle ExtractoR) is a program for extraction of torsion angle information from NMR data. Currently, it can analyze two types of input data: The torsion angle data, where several ³J-coupling constants and/or interatomic distances are combined in order to reduce the torsion angle ambiguity arising from solving the isolated Karplus (or distance) equation, and the sugar pucker data, where the dynamics of five-membered sugar rings is evaluated by postprocessing the results calculated from ³J_(HH) coupling constants by program PSEUROT. Program MULDER can be used either as an alternative to r-MD programs in situations where only specific structural features are studied, or as a preparatory tool in connection with full r-MD structure calculation for extraction of unambiguous torsion angle restraints.     

Penicillium roqueforti: a multifunctional cell factory of high value‐added molecules

This is a comprehensive review, with 114 references, of the chemical diversity found in the fungus Penicillium roqueforti. Secondary metabolites of an alkaloidal nature are described, for example, ergot alkaloids such as festuclavine, isofumigaclavines A and B, and diketopiperazine alkaloids such as roquefortines A–D, which are derived from imidazole. Other metabolites are marcfortines A–C, PR‐toxin, eremofortines A–E, mycophenolic and penicillic acids, and some γ‐lactones. Also, recent developments related to the structural characteristics of botryodiplodin and andrastin are studied—the latter has anticancer properties. Finally, we discuss the enzymes of P. roqueforti, which can participate in the biotechnological production of high value‐added molecules, as well as the use of secondary metabolite profiles for taxonomic purposes.     

Characterization and abolishment of the cyclopiazonic acids produced by Aspergillus oryzae HMP-F28

Extracellular alkalinization and H₂O₂ production are important early events during induced resistance establishment in plants. In a screen for metabolites as plant resistance activators from 98 fungal isolates associated with marine sponge Hymeniacidon perleve, the cyclopiazonic acids (CPAs) produced by Aspergillus oryzae HMP-F28 induced significant extracellular alkalinization coupled with augmented H₂O₂ production in tobacco cell suspensions. Bioassay-guided fractionation led to the isolation and structural elucidation of a new CPA congener (4, 3-hydroxysperadine A) and three known ones (1–3). To construct a mutasynthetic strain to generate unnatural CPA analogues, a hybrid pks-nrps gene (cpaS) was disrupted to abolish the production of the critical precursor of cyclo-acetoacetyl-L-tryptophan (cAATrp) and all the downstream CPA products. Elimination of cAATrp will allow cAATrp mimics being processed by the CPA biosynthetic machinery to produce CPA derivatives with designed structural features.     

Structural Basis for Topoisomerase I Inhibition by Nucleoside Analogs

Abstract

Nucleoside analogs such as 1-β-D-arabinofuranosyl cytidine (AraC) and 2′, 2′-difluoro deoxycytidine (dFdC) are important components of the anticancer chemotherapeutic arsenal and are among the most effective anticancer drugs currently available. Although both AraCTP and dFdCTP impede DNA replication through pausing of DNA polymerases, both nucleoside analogs are ultimately incorporated into replicated DNA and interfere in DNA-mediated processes. Our laboratories are investigating the structural basis for the poisoning of topoisomerase I (top1) due to antipyrimidine incorporation into duplex DNA. We recently reported that both AraC and dFdC induce formation of top1 cleavage complexes, and poisoning of top1 contributes to the anticancer activities of both these drugs. Recent NMR and thermodynamic studies from our laboratories provide insight into the mechanism by which AraC and dFdC poison top 1. NMR studies from our laboratories have revealed that the arabinosyl sugar of AraC adopted a C2′-endo conformation. Although this is a B-type sugar pucker characteristic of duplex DNA, the conformation is rigid, and this lack of flexibility probably contributes to inhibition of the religation step of the top 1 reaction. In contrast to AraC, NMR studies revealed dFdC adopted a C3′ endo sugar pucker characteristic of RNA, rather than DNA duplexes. dFdC substitution enhanced formation of top1 cleavage complexes, but did not inhibit religation. The enhancement of top1 cleavage complexes most likely results from a combination of conformational and electrostatic effects. The structural effects of dFdC and AraC are being further investigated in duplex DNA with well-defined top1 cleavage sites to analyze more specifically how these structural perturbations lead to enzyme poisoning.     

3-D Graphics Modelling of the tRNA-Like 3′-End of Turnip Yellow Mosaic Virus RNA: Structural and Functional Implications

Abstract

The tRNA-like structure of the aminoacylatable 3′-end of turnip yellow mosaic virus (TYMV) RNA was submitted to 3-D graphics modelling. A. model of this structure has been inferred previously from both biochemical results and sequence comparisons which presents a new RNA folding feature, the “pseudoknot”. It has been verified that this structure can be constructed without compromising accepted RNA stereochemical rules, namely base stacking and preferential 3′-endo sugar pucker. The model has aided interpretation of previous structural mapping experiments using chemical and enzymatic probes, and new accessibilities of residues could be predicted and tested.

Pseudoknots have been considered as potential splice sites because they form antiparallel helical segments in a single RNA molecule. We have examined this possibility with the constructed 3-D model and could verify the hypothesis on a structural basis.

The model presents a striking similarity with canonical tRNA and allows a valuable comparison between the protection patterns of yeast tRNA^Val and tRNA-like viral RNA by cognate yeast valyl-tRNA synthetase against structural probes.     

Role of Surface Glycolipids - Natural or Synthetic Origin on the Biodistribution of Liposomes

Abstract

Various sugar residues were incorporated on the surface of liposomes and its effect on the biodistribution and therapeutic importance were discussed here. Galactosylated liposomes were preferentially taken up by liver parenchymal cells whereas mannosylated liposomes were mainly localized in non-parenchyma1 cells. On the other hand, incorporation of dextran on the surface results in increased circulatory half-life of liposomes. The potential application of such liposomes as a carrier of drugs in the diseased condition is also discussed.     

Steroidal alkaloids from Holarrhena antidysenterica as acetylcholinesterase inhibitors and the investigation for structure-activity relationships

AimsInhibition of acetylcholinesterase (AChE) is still considered as a strategy for the treatment of neurological disorders such as Alzheimer's disease (AD). Many plant derived alkaloids (such as huperzine A, galanthamine and rivastigmine) are known for their AChE inhibitory activity. The aim of the present work was to isolate and identify new AChE inhibitors from Holarrhen antidysenterica.Main methodsThese compounds were tested for AChE inhibiting activity by the Ellman's method in 96-well microplates. In addition, molecular modeling was performed to explore the binding mode of inhibitors 1–5 at the active site of AChE, and the preliminary structure–activity relationships (SARs) were discussed.Key findingsIn the course of searching for AChE inhibitors from herb medicines, the total alkaloidal extract from the seeds of H. antidysenterica was found having potent AChE inhibitory activity with an IC₅₀ value of 6.1 μg/mL. Further bioactivity-guided chromatographic fractionation afforded five steroidal alkaloids, conessine 1, isoconessimine 2, conessimin 3, conarrhimin 4 and conimin 5. All the isolated compounds, except for 2, showed strong AChE inhibiting activity with IC₅₀ values ranging from 4 to 28 μM. The most active inhibitor is compound 3 with an IC₅₀ value of 4 μM. The mode of AChE inhibition by 3 was reversible and non-competitive.SignificanceThe results suggest that these alkaloids could be potential candidates for further development of new drugs against AD.     

Molecular Dynamics Study of Zinc-Blende GaN,AIN and InN

Abstract

We present a result of the molecular dynamics calculations with used a three-body empirical Tersoff potential. The parameters of the Tersoff potential are determined for nitride compound semiconductors such as GaN, AlN and InN. The structural and thermodynamic properties of GaN, AlN and InN in zinc-blende structure are presented. We report the equilibrium lattice constants, the bulk moduli, the cubic clastic constants, thermal expansion coefficient and specific heat. Good agreement is obtained with recent experimental and theoretical results for all constants.     

miR-34a在幼鼠海马神经元细胞增殖和凋亡中的作用

目的:探讨miR-34a在幼鼠海马神经元细胞增殖凋亡中的作用。方法:分离幼鼠海马神经元细胞,转染miR-34a抑制剂(miR-34a inhibitor)、抑制剂对照(inhibitor control)、miR-34a模拟物(miR-34a mimics)、模拟物对照(mimics control),RT-PCR检测细胞中miR-34a表达水平。MTT检测转染后细胞增殖情况。流式细胞仪检测细胞凋亡情况。Western blot检测细胞中Cleaved-caspase-3、Bcl-2、Bax的表达水平。结果:转染miR-34a inhibitor可以抑制miR-34a的表达,miR-34a mimics可以促进miR-34a的表达。miR-34a mimics对细胞增殖抑制率明显高于mimics control组(P0.05),miR-34a inhibitor组抑制率明显低于inhibitor control组(P0.05)。miR-34a inhibitor组神经元细胞凋亡率明显低于inhibitor control组(P0.05),miR-34a mimics组神经元细胞凋亡率明显高于mimics control组(P0.01),inhibitor control组和mimics control组神经元细胞凋亡率差异不显著(P0.05)。miR-34a inhibitor组Cleaved-caspase-3、Bax蛋白表达量低于inhibitor control组,差异显著(P0.05);miR-34a inhibitor组Bcl-2蛋白表达量高于inhibitor control组,差异显著(P0.05);miR-34a mimics组Cleaved-caspase-3、Bax蛋白表达量高于mimics control,差异显著(P0.05);miR-34a mimics组Bcl-2蛋白表达量低于mimics control,差异显著(P0.05)。结论:miR-34a抑制海马神经元细胞增殖,促进细胞凋亡,其作用机制可能与调控Cleaved-caspase-3、Bcl-2、Bax表达有关。     

非核糖体肽Skyllamycin B生物合成中I型硫酯酶底物杂泛性的初步研究

[背景] Skyllamycins是一类从链霉菌中发现的具有血小板生长因子抑制和生物膜抑制作用的非核糖体肽类,其环肽环合反应是由非核糖体肽合成酶中的硫酯酶功能域催化完成。[目的] 克隆和表达Skyllamycin非核糖体肽合成酶最后一个模块中的硫酯酶（Skyxy-TE）基因,合成Skyxy-TE底物类似物,通过体外催化实验表征Skyxy-TE的底物杂泛性。[方法] 采用Ligation Independent Cloning（LIC）方法,从一株含有Skyllamycin B生物合成基因簇的链霉菌Streptomyces sp.PKU-MA01239中克隆和表达skyxy-TE,通过镍离子柱亲和层析纯化Skyxy-TE。运用固相多肽合成法合成2个底物类似物1和2,进行Skyxy-TE的体外催化实验。[结果] 通过对Skyxy-TE的表达纯化,获得了纯度较好的可溶性蛋白;通过固相多肽合成,得到了能够模拟Skyllamycin B底物类似物的化合物1和2,硫酯酶蛋白体外催化化合物1和2得到了化合物3和4,化合物3和4通过核磁共振和高分辨质谱确认为环肽。[结论] Skyllamycin B生物合成中Skyxy-TE表现出一定的底物杂泛性,可以识别底物类似物催化环化反应,该研究为将来利用化学-酶联法制备更多环肽类似物提供了依据。     

Structural Advantage of Sugar Beet α-Glucosidase to Stabilize the Michaelis Complex with Long-chain Substrate

The α-glucosidase from sugar beet (SBG) is an exo-type glycosidase. The enzyme has a pocket-shaped active site, but efficiently hydrolyzes longer maltooligosaccharides and soluble starch due to lower K_m and higher k_cat/K_m for such substrates. To obtain structural insights into the mechanism governing its unique substrate specificity, a series of acarviosyl-maltooligosaccharides was employed for steady-state kinetic and structural analyses. The acarviosyl-maltooligosaccharides have a longer maltooligosaccharide moiety compared with the maltose moiety of acarbose, which is known to be the transition state analog of α-glycosidases. The clear correlation obtained between log K_i of the acarviosyl-maltooligosaccharides and log(K_m/k_cat) for hydrolysis of maltooligosaccharides suggests that the acarviosyl-maltooligosaccharides are transition state mimics. The crystal structure of the enzyme bound with acarviosyl-maltohexaose reveals that substrate binding at a distance from the active site is maintained largely by van der Waals interactions, with the four glucose residues at the reducing terminus of acarviosyl-maltohexaose retaining a left-handed single-helical conformation, as also observed in cycloamyloses and single helical V-amyloses. The kinetic behavior and structural features suggest that the subsite structure suitable for the stable conformation of amylose lowers the K_m for long-chain substrates, which in turn is responsible for higher specificity of the longer substrates.