Structural analysis and biological activities of C25-amino and C25-nitro vitamin D analogs.

Intense synthetic efforts have been directed towards the development of noncalcemic analogs of 1,25-dihydroxyvitamin D3. We describe here the structural analysis and biological evaluation of two derivatives of 1,25-dihydroxyvitamin D3 with modifications limited to the replacement of the 25-hydroxyl group by a 25-amino or 25-nitro groups. Both compounds are agonists of the vitamin D receptor. They mediate biological effects similar to 1,25-dihydroxyvitamin D3, the 25-amino derivative being the most potent one while being less calcemic than 1,25-dihydroxyvitamin D3. The in vivo properties of the compounds make them of potential therapeutic value.

On the mechanism of the dyotropic expansion of hydrindanes into decalins.

A combined computational/experimental approach has revealed key mechanistic aspects in a recently reported dyotropic expansion of hydrindanes into decalins. While computer simulations had already anticipated the need for acid catalysis for making this reaction feasible under the mild conditions used in the laboratory, this work places the dyotropic step not into the reaction flask but at a later step, during the work up instead. With this information in hand the reaction has been optimized by exploring the performance of different activating agents and shown to be versatile, particularly in steroid related chemistry due to the two scaffolds that this reaction connects. Finally, the scope of the reaction has been significantly broadened by showing that this protocol can also operate in the absence of the fused six-member ring.

Novel calcitriol analogue with an oxolane group: In vitro, in vivo, and in silico studies.

The active form of vitamin D3 , calcitriol, is a potent antiproliferative compound. However, when effective antitumor doses of calcitriol are used, hypercalcemic effects are observed, thus blocking its therapeutic application. To overcome this problem, structural analogues have been designed with the aim of retaining or even increasing the antitumor effects while decreasing its calcemic activity. This report aims at gaining insights into the structure-activity relationships of the novel oxolane-containing analogue, AM-27, recently synthesized. We herein demonstrate that this compound has antiproliferative and antimigratory effects in squamous cell carcinoma, glioblastoma, and breast cancer cell lines. Analyses of the mechanisms underlying the AM-27 effects on cell viability revealed induction of apoptosis by the analogue. Importantly, nonmalignant cell lines were little or not affected by the compound. In addition, the analogue did not produce hypercalcemia in mice. Also, in silico studies involving docking and molecular dynamics techniques showed that AM-27 is able to bind to the human vitamin D receptor with a higher affinity than the natural ligand calcitriol, a feature that is mostly derived from an electrostatic interaction pattern. Altogether, the proapoptotic effect observed in cancer cells, the lack of calcemic activity in mice, and the differential effects in normal cells suggest the potential of AM-27 as a therapeutic compound for cancer treatment.

Use of surface plasmon resonance in the binding study of vitamin D, metabolites and analogues with vitamin D binding protein.

Vitamin D3 and its metabolites are lipophilic molecules with low aqueous solubility and must be transported bound to plasma carrier proteins, primarily to vitamin D binding protein (DBP). The biological functions of vitamin D3 metabolites are intimately dependent on the protein, hence the importance of determining their affinity for DBP. In this study, we developed a novel procedure for measuring the kinetic and equilibrium constants of human-DBP with vitamin D3 and three metabolites: 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], 25-hydroxyvitamin D3 (25OHD3) and 24,25-dihydroxyvitamin D3 [24,25(OH)2D3] by surface plasmon resonance (SPR). At the same time, five different analogues, synthetized in our laboratory, were evaluated in order to compare the affinity values with the metabolites. Real-time SPR measurements showed that 25OHD3 and 24,25(OH)2D3 had higher affinity (0.3 µM) than 1,25(OH)2D3 (5 µM), with the higher affinity of 25OHD3 and 24,25(OH)2D3 due to dissociation constants 1 order of magnitude slower. In the case of the analogues, the affinity values were lower, with 1-hydroxy-25-nitro-vitamin D3 (NO2-446), structurally closer to 1,25(OH)2D3, showing the highest value with a K D of 50 µM. (24R)-1,25-dihydroxyvitamin-24-buthyl-28-norvitamin D2 (Bu-471) and (24R)-1,25-dihydroxyvitamin-24-phenyl-28-norvitamin D2 (Ph-491), structurally similar, had affinities of 180 and 170 µM, respectively. (22R,23E)-1-hydroxy-22-ethenyl-25-methoxy-23-dehydrovitamin D3 (MeO-455) and 1-hydroxy-20(R)-[5(S)-(2,2-dimethyltetrahydropyran-5-yl)]-22,23-dinor vitamin D3 (Oxan-429) had affinities of 310 and 100 µM, respectively. The binding of the metabolites and analogues was reversible allowing the rapid capture of data for replicates. The kinetic and equilibrium data for both the metabolites and the analogues fitted to the Langmuir model describing a 1:1 interaction. Graphical Abstract Label-free, real time binding study between vitamin D binding protein immmobilized on the surface of a SPR sensor chip and the vitamin D, metabolites and analogues passed over it as analytes.

Vitamin D analogue: potent antiproliferative effects on cancer cell lines and lack of hypercalcemic activity.

The active form of vitamin D3, 1α,25(OH)2D3, plays a major role in maintaining calcium/phosphate homeostasis. In addition, it is a potent antiproliferative and pro-differentiating agent. Unfortunately, it usually causes hypercalcemia in vivo when effective antitumour doses are used. It has therefore been found necessary to synthesise new analogues that retain or even increase the antitumour effects but preclude hypercalcemia. This report presents the synthesis of a novel Gemini vitamin D analogue (UVB1) and its biological evaluation. We demonstrate that this compound has potent antitumoural effects over a wide panel of tumour cell lines while showing lack of hypercalcemic activity and toxicity effects in in vivo assays.

Design, Synthesis, and Biological Evaluation of New Type of Gemini Analogues with a Cyclopropane Moiety in Their Side Chain.

We synthesized two new gemini analogues, UG-480 and UG-481, that incorporate a modified longer side chain containing a cyclopropane group. The evaluation of the bioactivities of the two gemini analogues indicated that the 17,20 threo (20S) compound, UG-480, is the most active one and is as active as 1,25(OH)2D3. Docking and molecular dynamics (MD) data showed that the compounds bind efficiently to vitamin D receptor (VDR) with UG-480 to form an energetically more favorable interaction with His397. Structural analysis indicated that whereas the UG-480 compound efficiently stabilizes the active VDR conformation, it induces conformational changes in the H6-H7 VDR region that are greater than those induced by the parental Gemini and that this is due to the occupancy of the secondary channel by its modified side chain.

Synthesis and biological evaluation of a new vitamin D2 analogue.

A new vitamin D(2) analogue was synthesized using the Julia-Kocienski olefination. It has antiproliferative effects on cell lines from squamous cell carcinomas of colon and head and neck, but is also as hypercalcaemic as calcitriol in vivo.

First computational chemistry multi-target model for anti-Alzheimer, anti-parasitic, anti-fungi, and anti-bacterial activity of GSK-3 inhibitors in vitro, in vivo, and in different cellular lines.

In the work described here, we developed the first multi-target quantitative structure-activity relationship (QSAR) model able to predict the results of 42 different experimental tests for GSK-3 inhibitors with heterogeneous structural patterns. GSK-3ß inhibitors are interesting candidates for developing anti-Alzheimer compounds. GSK-3ß are also of interest as anti-parasitic compounds active against Plasmodium falciparum, Trypanosoma brucei, and Leishmania donovani; the causative agents for Malaria, African Trypanosomiasis and Leishmaniosis. The MARCH-INSIDE technique was used to quickly calculate total and local polarizability, n-octanol/water partition coefficients, refractivity, van der Waals area and electronegativity values to 4,508 active/non-active compounds as well as the average values of these indexes for active compounds in 42 different biological assays. Both the individual molecular descriptors and the average values for each test were used as input for a linear discriminant analysis (LDA). We discovered a classification function which used in training series correctly classifies 873 out of 1,218 GSK-3 cases of inhibitors (97.4%) and 2,140 out of 2,163 cases of non-active compounds (86.1%) in the 42 different tests. In addition, the model correctly classifies 285 out of 406 GSK-3 inhibitors (96.3%) and 710 out of 721 cases of non-active compounds (85.4%) in external validation series. The result is important because, for the first time, we can use a single equation to predict the results of heterogeneous series of organic compounds in 42 different experimental tests instead of developing, validating, and using 42 different QSAR models. Lastly, a double ordinate Cartesian plot of cross-validated residuals (first ordinate), standard residuals (second ordinate), and leverages (abscissa) defined the domain of applicability of the model as a squared area within ± 2 band for residuals and a leverage threshold of h = 0.0044.

Theoretical study of GSK-3α: neural networks QSAR studies for the design of new inhibitors using 2D descriptors.

Glycogen synthase kinase-3 (GSK-3) targets encompass proteins implicated in AD and neurological disorders. The functions of GSK-3 and its implication in various human diseases have triggered an active search for potent and selective GSK-3 inhibitors. In this sense, QSAR could play an important role in studying these GSK-3 inhibitors. For this reason, we developed QSAR models for GSK-3α, linear discriminant analysis (LDA), and artificial neural networks (ANNs) from nearly 50,000 cases with more than 700 different GSK-3α inhibitors obtained from ChEMBL database server; in total we used more than 20,000 different molecules to develop the QSAR models. The model correctly classified 237 out of 275 active compounds (86.2%) and 14,870 out of 15,970 non-active compounds (93.2%) in the training series. The overall training performance was 93.0%. Validation of the model was carried out using an external predicting series. In these series, the model classified correctly 458 out of 549 (83.4%) compounds and 29,637 out of 31,927 non-active compounds (83.4%). The overall predictability performance was 92.7%. In this study, we propose three types of non-linear ANN as alternative to already existing models, such as LDA. Linear neural network: LNN: 236:236-1-1:1 which had an overall training performance of 96% proved to be the best model. In addition, we did a study of the different fragments of the molecules of the database to see which fragments had more influence in the activity. This can help design new inhibitors of GSK-3α. This study reports the attempts to calculate, within a unified framework probabilities of GSK-3α inhibitors against different molecules found in the literature.

Vitamin D analogues exhibit antineoplastic activity in breast cancer patient-derived xenograft cells.

Despite advances in breast cancer (BC) treatment, its mortality remains high due to intrinsic or acquired resistance to therapy. Several ongoing efforts are being made to develop novel drugs to treat this pathology with the aim to overcome resistance, prolong patient survival and improve their quality of life. We have previously shown that the non-hypercalcemic vitamin D analogues EM1 and UVB1 display antitumor effects in preclinical studies employing conventional cell lines and animal models developed from these cells. In this work, we explored the antitumor effects of EM1 and UVB1 employing BC cells derived from patient-derived xenografts (PDXs), which are a powerful preclinical tool for testing new drugs. We demonstrated that the analogues reduced the viability of HER2-positive and Triple Negative BC-PDXs. Moreover, using an in vitro model of acquired resistance to Trastuzumab-emtansine, UVB1 displayed anti-proliferative actions under 2D and 3D culture conditions. It inhibited both formation and growth of established organoids. In addition, a direct correlation between UVB1 antitumor effects and VDR expression in PDXs was found. In conclusion, all the results reinforce the potential use of these vitamin D analogues as antitumor agents to treat HER2-positive and Triple Negative BC.

Using topological indices to predict anti-Alzheimer and anti-parasitic GSK-3 inhibitors by multi-target QSAR in silico screening.

Plasmodium falciparum, Leishmania, Trypanosomes, are the causers of diseases such as malaria, leishmaniasis and African trypanosomiasis that nowadays are the most serious parasitic health problems worldwide. The great number of deaths and the few drugs available against these parasites, make necessary the search for new drugs. Some of these antiparasitic drugs also are GSK-3 inhibitors. GSKI-3 are candidates to develop drugs for the treatment of Alzheimer's disease. In this work topological descriptors for a large series of 3,370 active/non-active compounds were initially calculated with the ModesLab software. Linear Discriminant Analysis was used to fit the classification function and it predicts heterogeneous series of compounds like paullones, indirubins, meridians, etc. This study thus provided a general evaluation of these types of molecules.

Easy Access to Polyfunctionalized Chiral Decalins.

An unexpected ring expansion that converts hydrindanes into decalins via an unprecedented dyotropic reaction involving a mesylate group has been observed, and this paved the way for easy access to polyfunctionalized chiral decalins. These polyfunctionalized chiral decalins can be very useful building blocks for the synthesis of the thia analogues of many natural compounds. They can also be used in asymmetric catalysis and also in the synthesis of the new analogues of vitamin D with a modified D ring and side chain. The use of chiral sulfoxide ligands for asymmetric catalysis or asymmetric sulfur ylide-mediated epoxidation of carbonyl compounds is a very important topic in the field of organic chemistry, hence our results could be useful to the scientific community.

Vitamin D receptor exhibits different pharmacodynamic features in tumoral and normal microenvironments: A molecular modeling study.

The vitamin D receptor (VDR) constitutes a promising therapeutic target for the treatment of cancer. Unfortunately, its natural agonist calcitriol does not have clinical utility due to its potential to induce hypercalcemic effects at the concentrations required to display antitumoral activity. For this reason, the search for new calcitriol analogues with adequate therapeutic profiles has been actively pursued by the scientific community. We have previously reported the obtaining and the biological activity evaluation of new calcitriol analogues by modification of its sidechain, which exhibited relevant antiproliferative and selectivity profiles against tumoral and normal cells. In this work we conducted molecular modeling studies (i.e. molecular docking, molecular dynamics, constant pH molecular dynamics (CpHMD) and free energy of binding analysis) to elucidate at an atomistic level the molecular basis related to the potential of the new calcitriol analogues to achieve selectivity between tumoral and normal cells. Two histidine residues (His305 and His397) were found to exhibit a particular tautomeric configuration that produces the observed bioactivity. Also, different acid-based properties were observed for His305 and His307 with His305 showing an increased acidity (pKa 5.2) compared to His397 (pKa 6.8) and to the typical histidine residue. This behavior favored the pharmacodynamic interaction of the calcitriol analogues exhibiting selectivity for tumoral cells when VDR was modeled at the more acidic tumoral environment (pH ≅ 6) compared to the case when VDR was modeled at pH 7.4 (normal cell environment). On the other hand, non-selective compounds, including calcitriol, exhibited a similar interaction pattern with VDR when the receptor was modeled at both pH conditions. The results presented constitute the first evidence on the properties of the VDR receptor in different physicochemical environments and thus represent a significant contribution to the in silico screening and design of new calcitriol analogues.

Access to a Library of 1,3-disubstituted-1,2,3-triazenes and Evaluation of their Antimicrobial Properties.

BACKGROUND: Due to the rapid development of microbial resistance, finding new molecules became urgent to counteract this problem. OBJECTIVE: The objective of this work is to access 1,2,3-triazene-1,3-disubstituted, a class of molecule with high therapeutic potential. METHODS: Here we describe the access to 17 new triazene including six with an imidazole-1,2,3-triazene moiety and eleven with an alkyl-1,2,3-triazene moiety and their evaluation against five strains: two gram (-): Escherichia coli ATCC 25921 and Pseudomonas aeruginosa ATCC 27253; two gram (+) : Staphylococcus aureus ATCC 38213 and Enterococcus faecalis ATCC 29212; and one fungi: Candida albicans ATCC 24433. RESULTS: All strains were sensitive and the best MIC, 0.28 µM, is observed for 4c against Escherichia coli ATCC 25921. Compound 9, 3-isopropynyltriazene, appears to be the most interesting since it is active on the five evaluated strains with satisfactory MIC 0.32 µM against Escherichia coli and Pseudomonas aeruginosa and 0.64 µM against Enterococcus faecalis and Pseudomonas aeruginosa. CONCLUSION: Comparing the structure activity relationship, electron withdrawing groups appear to increase antimicrobial activity.

The first enantioselective synthesis of palinurin.

The first enantioselective synthesis of palinurin has been accomplished starting from commercially available furaldehyde and (R)-methyl-3-hydroxy-2-methylpropionate; the key steps of the synthesis include the use of a chiral pyrrolidine to create the chiral tetronic moiety, and Horner-Wadsworth-Emmons, Wittig and Wittig-Horner reactions to construct the alkene units.

QSAR and complex network study of the chiral HMGR inhibitor structural diversity.

Efficient drugs such as statins or mevinic acids are inhibitors of the rate-limiting enzyme of cholesterol biosynthesis, 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGR), an enzyme responsible for the double reduction of 3-hydroxy-3-methyl-glutaryl coenzyme A into mevalonic acid. These compounds promoted the synthesis and evaluation of new inhibitors for HMGR, named HMGRIs. The high number of possible candidates creates the necessity of Quantitative Structure-Activity Relationship models in order to guide the HMGRI synthesis. There are two main problems of the reported QSAR models: the homogeneous series of the compounds and the chirality of many candidates. In this work, we propose for the first time a QSAR model for a very large and heterogeneous series of HMGRIs. The model is based on the Topological Indices (TIs) of molecular structures. Using the predictions of this model as input, we construct the first complex network that describes the drug-drug similarity relationships for more than 1600 experimentally non-explored chiral HMGRIs isomers. We also presented a reduced version of this network (Giant Component) that contains the most representative set of chiral HMGRI candidates. The work suggests a new mixed application in the QSAR study of relevant aspects of structural diversity by using chiral/non-chiral TIs, combined with complex networks.

Synthesis of a novel analog of calcitriol and its biological evaluation as antitumor agent.

Calcitriol analogs have shown promising potential as compounds to be used in cancer chemotherapy. This report presents the synthesis of a novel vitamin D3 derivative with an amide and a carboxyl group in its side chain, called ML-344. In addition, we report its in vitro antitumor activity and its in vivo calcemic effects. We demonstrate that the analog decreases cell viability and retards cell migration of different breast, glioblastoma and head and neck cancer cell lines. Additionally, unlike calcitriol, ML-344 does not display citotoxicity to the murine non-malignant mammary cells and human astrocytes. In concordance with the antimigratory effects found in breast cancer cells, ML-344 decreased the invasive capacity and induced a rearrangement of the actin cytoskeleton in the LM3 breast cancer cell line. In relation to the in vivo studies, the analog did not cause hypercalcemic effects in CF1 mice administered daily at 5 µg/Kg of body weight during a period of 264 h. Finally, computational studies were performed to evaluate the potential binding of the analog to the vitamin D receptor and the in silico assays showed that ML-344 is able to bind to VDR with interesting particularities and greater affinity than calcitriol. Altogether, these results suggest that ML-344 has a promising potential as an antitumor agent with a differential effect between tumor and non-malignant cells.

Radial Distribution Function descriptors for predicting affinity for vitamin D receptor.

The QSAR is an alternative method for the research of new and better Vitamin D analogues with affinity for the VDR receptor. This paper describes the results of applying the Radial Distribution Function (RDF descriptors) approach for predicting the VDR affinity of 38 vitamin D analogues. The model described 80% of the experimental variance, with a standard deviation of 0.35. Leave-one-out, bootstrapping and external set validation were carried out with the aim of evaluating the predictive power of the model. The values of their respective squared correlations coefficients were 0.72, 0.70 and 0.79. The RDF approach was compared with four other predictive models, but none of these could explain more than 71.0% of the variance with six variables in their respective models.

Antitumoral effects of the alkynylphosphonate analogue of calcitriol EM1 on glioblastoma multiforme cells.

Glioblastoma multiforme (GBM) is the worst and most common brain tumor, characterized by high proliferation and invasion rates. The current standard treatment is mainly based on chemoradiotherapy and this approach has slightly improved patient survival. Thus, novel strategies aimed at prolonging the survival and ensuring a better quality of life are necessary. In the present work, we investigated the antitumoral effect of the novel analogue of calcitriol EM1 on GBM cells employing in vitro, in silico, and in vivo assays. In vitro, we demonstrated that EM1 treatment selectively decreases the viability of murine and human tumor cells without affecting that of normal human astrocytes. The analysis of the mechanisms showed that EM1 produces cell cycle arrest in the T98G cell line, which is accompanied by an increase in p21, p27, p57 protein levels and a decrease in cyclin D1, p-Akt-S473, p-ERK1/2 and c-Jun expression. Moreover, EM1 treatment also exerts in GBM cells anti-migratory effects and decreases their invasive capacity by a reduction in MMP-9 proteolytic activity. In silico, we demonstrated that EM1 is able to bind to the vitamin D receptor with greater affinity than calcitriol. Finally, we showed that EM1 treatment of nude mice administered at 50ug/kg body weight during 21days neither induces hypercalcemia nor toxicity effects. In conclusion, all the results indicate the potential of EM1 analogue as a promising therapeutic alternative for GBM treatment.

Quantitative structure-activity relationship studies of HIV-1 integrase inhibition. 1. GETAWAY descriptors.

The GEometry, Topology, and Atom-Weights AssemblY (GETAWAY) approach has been applied to the study of the HIV-1 integrase inhibition of 172 compounds that belong to 11 different chemistry families. A model able to describe more than 68.5% of the variance in the experimental activity was developed with the use of the mentioned approach. In contrast, none of the five different approaches, including the use of Randic Molecular Profiles, Geometrical, RDF, 3D-MORSE and WHIM descriptors was able to explain more than 62.4% of the variance in the mentioned property with the same number of variables in the equation. Finally, after extracting five compounds considered by us as outliers the model was able to describe more than 72.5% of the variance in the experimental activity.