Applications of biaryl cyclization in the synthesis of cyclic enkephalin analogs with a highly restricted flexibility.

A series of 10 cyclic, biaryl analogs of enkephalin, with Tyr or Phe residues at positions 1 and 4, were synthesized according to the Miyaura borylation and Suzuki coupling methodology. Biaryl bridges formed by side chains of the two aromatic amino acid residues are of the meta-meta, meta-para, para-meta, and para-para configuration. Conformational properties of the peptides were studied by CD and NMR. CD studies allowed only to compare conformations of individual peptides while NMR investigations followed by XPLOR calculations provided detailed information on their conformation. Reliability of the XPLOR calculations was confirmed by quantum chemical ones performed for one of the analogs. No intramolecular hydrogen bonds were found in all the peptides. They are folded and adopt the type IV ß-turn conformation. Due to a large steric strain, the aromatic carbon atoms forming the biaryl bond are distinctly pyramidalized. Seven of the peptides were tested in vitro for their affinity for the µ-opioid receptor.

Synthesis And Anticancer Activity Of New Hybrid 3-Methylidene-2,3-Dihydro-1,8-Naphthyridinones.

Synthesis of molecular hybrids, obtained by combination of two or more pharmacophoric groups of different bioactive substances in order to produce more efficient drugs, is now a frequently used approach in medicinal chemistry. Following this strategy, we synthetized a library of 3-methylidene-1-tosyl-2,3-dihydro-1,8-naphthyridin-4(1H)-ones, combining a 1,8-naphthyridin-4-one motif with an exo-methylidene bond conjugated with a carbonyl group, pharmacophoric units that are present in many natural, biologically active compounds with anticancer potential. We reasoned that such bifunctional conjugates may have enhanced cytotoxic activity. The title compounds were synthesized in a four step reaction sequence. ß-Ketophosphonate, obtained from methyl N-tosylnicotinate and diethyl methylphosphonate, was reacted with various aldehydes giving 3-diethoxyphosphoryl-2,3-dihydro-1,8-naphthyridin-4(1H)-ones as keto-enol tautomers. Later, these compounds were transformed into 3-methylidene-1-tosyl-2,3-dihydro-1,8-naphthyridin-4(1H)-ones applying the Horner-Wadsworth-Emmons methodology. Then, the cytotoxicity of the new compounds was assessed on two cancer cell lines, promyelocytic leukemia HL-60 and breast cancer adenocarcinoma MCF-7, and for comparison, on human umbilical vein endothelial cells HUVEC. The most active and selective analog, 2-ethyl-3-methylidene-1-tosyl-2,3-dihydro-1,8-naphthyridin-4(1H)-one 4 a was chosen for more detailed studies on HL-60 cell line, to determine molecular mechanisms of its anticancer activity. It was shown that 4 a strongly inhibited proliferation and induced apoptosis which could be attributed to its ability to cause DNA damage.

Moving out of CF3 -Land: Synthesis, Receptor Affinity, and in silico Studies of NK1 Receptor Ligands Containing a Pentafluorosulfanyl (SF5 ) Group.

The NK1 receptor (NK1R) is a molecular target for both approved and experimental drugs intended for a variety of conditions, including emesis, pain, and cancers. While contemplating modifications to the typical NK1R pharmacophore, we wondered whether the CF3 groups common for many NK1R ligands, could be replaced with some other moiety. Our attention was drawn by the SF5 group, and so we designed, synthesized, and tested ten novel SF5 -containing compounds for NK1R affinity. All analogues exhibit detectable NK1R binding, with the best of them, compound 5 a, (3-bromo-5-(pentafluoro-λ6 -sulfanyl)benzyl acetyl-L-tryptophanate) binding only slightly worse (IC50 =34.3 nM) than the approved NK1R-targeting drug, aprepitant (IC50 =27.7 nM). Molecular docking provided structural explanation of SAR. According to our analysis, the SF5 group in our compounds occupies a position similar to that of one of the CF3 groups of aprepitant as found in the crystal structure. Additionally, we checked whether the docking scoring function or energies derived from Fragment Molecular Orbital quantum chemical calculations may be helpful in explaining and predicting the experimental receptor affinities for our analogues. Both these methods produce moderately good results. Overall, this is the first demonstration of the utility of the SF5 group in the design of NK1R ligands.

The influence of a synthetic growth hormone-releasing hormone analogue G11 and opioid peptide biphalin on selected fibroblasts parameters relevant to wound healing.

The treatment of hard-to-heal chronic wounds is still a major medical problem and an economic and social burden. In this work, we examine the proregenerative potential of two peptides, G11 (a trypsin-resistant analogue of growth hormone-releasing hormone [GHRH]) and biphalin (opioid peptide), and their combination in vitro on human fibroblasts (BJ). G11, biphalin and their combination exhibited no toxicity against BJ cells. On the contrary, these treatments significantly stimulated proliferation and migration of fibroblasts. Under inflammatory conditions (LPS-induced BJ cells), we noticed that the tested peptides decreased the levels of cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS) and interleukin 1ß (IL-1ß). This was correlated with diminished phosphorylation levels of p38 kinase, but not those of ERK1/2. We found also that G11, biphalin and their combination activated the ERK1/2 signalling pathway, which has been previously implicated in promigratory activity of some regeneration enhancers, including opioids or GHRH analogues. Potential application of their combination requires further work, in particular in vivo experiments, in which the organism-level relevance of the discussed cell-level effects would be proven and, additionally, analgesic action of the opioid ingredient could be quantified.

Gαi-derived peptide binds the µ-opioid receptor.

BACKGROUND: G protein-coupled receptors (GPCRs) transduce external stimuli into the cell by G proteins via an allosteric mechanism. Agonist binding to the receptor stimulates GDP/GTP exchange within the heterotrimeric G protein complex, whereas recent structures of GPCR-G protein complexes revealed that the H5, S1 and S2 domains of Gα are involved in binding the active receptor, earlier studies showed that a short peptide analog derived from the C-terminus (H5) of the G protein transducin (Gt) is sufficient to stabilize rhodopsin in an active form. METHODS: We have used Molecular Dynamics simulations along with biological evaluation by means of radio-ligand binding assay to study the interactions between Gαi-derived peptide (G-peptide) and the µ-opioid receptor (µOR). RESULTS: Here, we show that a Gαi-derived peptide of 12 amino acids binds the µ-opioid receptor and acts as an allosteric modulator. The Gαi-derived peptide increases µOR affinity for its agonist morphine in a dose-dependent way. CONCLUSIONS: These results indicate that the GPCR-Gα peptide interaction observed so far for only rhodopsin can be extrapolated to µOR. In addition, we show that the C-terminal peptide of the Gαi subunit is sufficient to stabilize the active conformation of the receptor. Our approach opens the possibility to investigate the GPCR-G protein interface with peptide modification.

Docking is not enough: 17-trifluoromethylphenyl trinor PGF2α is only a very weak ligand of neurokinin-1 receptor.

17-trifluoromethylphenyl trinor prostaglandin F2α (17-CF3PTPGF2α) was reported recently to exhibit in vitro and in vivo anticancer activity. Based solely on the results of in silico molecular docking, it was claimed that this compound is NK1 receptor (NK1R) antagonist and that its activity is through this receptor. In this contribution we show that 17-CF3PTPGF2α is only a very weak NK1R ligand (IC50 > 200 µM). In connection with that we discuss the issue of this compound's molecular target. Finally, we briefly narrate on the proper use of molecular docking in biomedical research.

Improving short-term water demand forecasting using evolutionary algorithms.

Modern solutions in water distribution systems are based on monitoring the quality and quantity of drinking water. Identifying the volume of water consumption is the main element of the tools embedded in water demand forecasting (WDF) systems. The crucial element in forecasting is the influence of random factors on the identification of water consumption, which includes, among others, weather conditions and anthropogenic aspects. The paper proposes an approach to forecasting water demand based on a linear regression model combined with evolutionary strategies to extract weekly seasonality and presents its results. A comparison is made between the author's model and solutions such as Support Vector Regression (SVR), Multilayer Perceptron (MLP), and Random Forest (RF). The implemented daily forecasting procedure allowed to minimize the MAPE error to even less than 2% for water consumption at the water supply zone level, that is the District Metered Area (DMA). The conducted research may be implemented as a component of WDF systems in water companies, especially at the stage of data preprocessing with the main goal of improving short-term water demand forecasting.

Correcting a widespread error: Neuroprotectant N-acetyl-L-tryptophan does not bind to the neurokinin-1 receptor.

N-acetyl-L-tryptophan (NAT) has been often shown to have neuroprotective action and other biological activities. In many of papers devoted to this compound, NAT is referenced to as an 'NK1 receptor (NK1R) antagonist' or a 'substance P (SP) antagonist'. Some of the studies treated NAT as a tool compound to interrogate NK1R function in a particular condition. Surprisingly however, no biochemical data on NAT/NK1R interaction have been available. On testing NAT in radioligand receptor binding assay, we found that this compound displays no significant binding to either human or rat NK1R up to millimolar concentrations. In light of this, the repeated claim of NAT being NK1R antagonist is an error. The use of NAT as a tool compound in NK1R-related studies should be discontinued. Some of the conclusions regarding the involvement of SP/NK1R axis in acute CNS injury or neurodegenerative diseases may then require careful rethinking. On the other hand, given interesting neuroprotective properties of NAT, the issue whether it acts by specific interactions with some molecular target or by unspecific physicochemical mechanisms needs be investigated.

Fentanyl Structure as a Scaffold for Opioid/Non-Opioid Multitarget Analgesics.

One of the strategies in the search for safe and effective analgesic drugs is the design of multitarget analgesics. Such compounds are intended to have high affinity and activity at more than one molecular target involved in pain modulation. In the present contribution we summarize the attempts in which fentanyl or its substructures were used as a µ-opioid receptor pharmacophoric fragment and a scaffold to which fragments related to non-opioid receptors were attached. The non-opioid 'second' targets included proteins as diverse as imidazoline I2 binding sites, CB1 cannabinoid receptor, NK1 tachykinin receptor, D2 dopamine receptor, cyclooxygenases, fatty acid amide hydrolase and monoacylglycerol lipase and σ1 receptor. Reviewing the individual attempts, we outline the chemistry, the obtained pharmacological properties and structure-activity relationships. Finally, we discuss the possible directions for future work.

In Vitro Biological Evaluation of Aprepitant Based 177Lu-Radioconjugates.

Currently, the search for promising NK1R-positive tumor-targeting radiopharmaceuticals based on the structure of small molecular antagonists of neurokinin-1 receptor can be observed. Following this trend, we continued our evaluation of aprepitant-based 177Lu-radioconjugates in terms of future oncological applications. For this purpose, three novel aprepitant homologues were synthesized to broaden the previously obtained derivative portfolio, functionalized with the DOTA chelator and labeled with 68Ga and 177Lu. The newly evaluated radioconjugates showed the intended significant increase in lipophilicity compared to the previous ones, while maintaining stability in the human serum. Then, in a receptor binding study to the human NK1 receptor, we compared the two series of 177Lu-radioconjugates of aprepitant with each other and with the reference Substance P derivative currently used in glioblastoma therapy, clearly indicating the high affinity and better binding capacity of the novel radioconjugates. The in vitro experimental results included in the presented study, supported by labeling optimization, radioconjugate characterization and docking modeling of new aprepitant-derived radioagents, confirm our assumptions about the usefulness of aprepitant as a NK1R targeting vector and point out the perspectives for the forthcoming first in vivo trials.

The View Outside of the Box: Reporting Outcomes Following Radical Cystectomy Using Pentafecta From a Multicenter Retrospective Analysis.

We aimed at characterization of the patients undergoing radical cystectomy (RC) using the prognostic model (a modified pentafecta). In the multicenter retrospective study, we enrolled 304 patients with bladder cancer (pTis-4N0-2M0) who underwent RC between 2015 and 2020 in experienced centers. The definition of the pentafecta was as follows: no Clavien-Dindo grade III-V complications at 90 days and no long-term complications related to urinary diversion <12 months, negative surgical margins, ≥10 lymph nodes (LNs) resected, and no recurrence ≤12 months. RC-pentafecta achievement rate was 22% (n = 67), varying from 47% to 88% attainment rate for different pentafecta components, and was the lowest for sufficient LN yield. Both 12-month recurrence-free survival (RFS) and cancer-specific mortality were compromised in pentafecta failers compared with achievers (57.8% vs. 100% and 33.8% vs. 1.5%, respectively). The following were identified as crucial predictors of RC pentafecta achievement: modality of the surgery, type of urinary diversion, histological type of bladder cancer, advanced staging, and elevated preoperative serum creatinine. In conclusion, we found that the pentafecta achievement rate was low even in high-volume centers in patients undergoing cystectomy. The complexity of the procedure directly influenced the attainment rate, which in turn led to an increase in cancer-specific mortality rate among the pentafecta failers.

Novel NK1R-Targeted 68Ga-/177Lu-Radioconjugates with Potential Application against Glioblastoma Multiforme: Preliminary Exploration of Structure-Activity Relationships.

Locoregionally administered, NK1 receptor (NK1R) targeted radionuclide therapy is a promising strategy for the treatment of glioblastoma multiforme. So far, the radiopharmaceuticals used in this approach have been based on the endogenous agonist of NK1R, Substance P or on its close analogues. Herein, we used a well-known, small molecular NK1R antagonist, L732,138, as the basis for the radiopharmaceutical vector. First, 14 analogues of this compound were evaluated to check whether extending the parent structure with linkers of different lengths would not deteriorate the NK1R binding. The tested analogues had affinity similar to or better than the parent compound, and none of the linkers had a negative impact on the binding. Next, five DOTA conjugates were synthesized and used for labelling with 68Ga and 177Lu. The obtained radioconjugates turned out to be fairly lipophilic but showed rather limited stability in human plasma. Evaluation of the receptor affinity of the (radio)conjugates showed that neither the chelator nor the metal negatively impacts the NK1R binding. The 177Lu-radioconjugates exhibited the binding characteristics towards NK1R similar or better than that of the 177Lu-labelled derivative of Substance P, which is in current clinical use. The experimental results presented herein, along with their structural rationalization provided by modelling, give insight for the further molecular design of small molecular NK1R-targeting vectors.

Bifunctional Opioid/Melanocortin Peptidomimetics for Use in Neuropathic Pain: Variation in the Type and Length of the Linker Connecting the Two Pharmacophores.

Based on the mechanism of neuropathic pain induction, a new type of bifunctional hybrid peptidomimetics was obtained for potential use in this type of pain. Hybrids consist of two types of pharmacophores that are connected by different types of linkers. The first pharmacophore is an opioid agonist, and the second pharmacophore is an antagonist of the pronociceptive system, i.e., an antagonist of the melanocortin-4 receptor. The results of tests in acute and neuropathic pain models of the obtained compounds have shown that the type of linker used to connect pharmacophores had an effect on antinociceptive activity. Peptidomimetics containing longer flexible linkers were very effective at low doses in the neuropathic pain model. To elucidate the effect of linker lengths, two hybrids showing very high activity and two hybrids with lower activity were further tested for affinity for opioid (mu, delta) and melanocortin-4 receptors. Their complexes with the target receptors were also studied by molecular modelling. Our results do not show a simple relationship between linker length and affinity for particular receptor types but suggest that activity in neuropathic pain is related to a proper balance of receptor affinity rather than maximum binding to any or all of the target receptors.

The solid state VCD of a novel N-acylhydrazone trifluoroacetate.

A novel N-acylhydrazone with pharmaceutical importance was subject of structural and IR/VCD investigations in the solid state. In the crystal structure, dimers of anion-cation pairs are stabilized by H-bonding and ionic interactions. Some less common interaction types, like C=N···C-NH3+ (σ-hole) interactions, hydrazone-aromatic interactions and dispersive contacts of the CF3 groups are also present in the crystal. Satisfactory reproduction of the solid state IR and VCD spectra required that quantum-chemical calculations be done on a tetramer (four cation-anion pairs) cut out from the crystal structure, exhibiting key intermolecular interactions. Ten DFT functionals were assessed as to the agreement between the calculated and experimental spectra. Various approaches to scaling of the calculated frequencies were applied. The best results were yielded with individual (optimized) frequency scaling factors (FSFs) and band half-widths at half maximum-(HWHM) for four separate spectral subregions. The best matching between the experimental and theoretical spectra (according to SimIR, SimVCD and SimVDF indices) was found for the B3PW91 functional, however, a few other functionals follow closely in the ranking. Based on the quantum chemical calculations, spectral assignments have been made.

PSMA-D4 Radioligand for Targeted Therapy of Prostate Cancer: Synthesis, Characteristics and Preliminary Assessment of Biological Properties.

A new PSMA ligand (PSMA-D4) containing the Glu-CO-Lys pharmacophore connected with a new linker system (L-Trp-4-Amc) and chelator DOTA was developed for radiolabeling with therapeutic radionuclides. Herein we describe the synthesis, radiolabeling, and preliminary biological evaluation of the novel PSMA-D4 ligand. Synthesized PSMA-D4 was characterized using TOF-ESI-MS, NMR, and HPLC methods. The novel compound was subject to molecular modeling with GCP-II to compare its binding mode to analogous reference compounds. The radiolabeling efficiency of PSMA-D4 with 177Lu, 90Y, 47Sc, and 225Ac was chromatographically tested. In vitro studies were carried out in PSMA-positive LNCaP tumor cells membranes. The ex vivo tissue distribution profile of the radioligands and Cerenkov luminescence imaging (CLI) was studied in LNCaP tumor-bearing mice. PSMA-D4 was synthesized in 24% yield and purity >97%. The radio complexes were obtained with high yields (>97%) and molar activity ranging from 0.11 to 17.2 GBq mcmol-1, depending on the radionuclide. In vitro assays confirmed high specific binding and affinity for all radiocomplexes. Biodistribution and imaging studies revealed high accumulation in LNCaP tumor xenografts and rapid clearance of radiocomplexes from blood and non-target tissues. These render PSMA-D4 a promising ligand for targeted therapy of prostate cancer (PCa) metastases.

Synthesis, Pharmacological Evaluation, and Computational Studies of Cyclic Opioid Peptidomimetics Containing ß3-Lysine.

Our formerly described pentapeptide opioid analog Tyr-c[D-Lys-Phe-Phe-Asp]NH2 (designated RP-170), showing high affinity for the mu (MOR) and kappa (KOR) opioid receptors, was much more stable than endomorphine-2 (EM-2) in the rat brain homogenate and displayed remarkable antinociceptive activity after central (intracerebroventricular) and peripheral (intravenous ) administration. In this report, we describe the further modification of this analog, which includes the incorporation of a ß3-amino acid, (R)- and (S)-ß3-Lys, instead of D-Lys in position 2. The influence of such replacement on the biological properties of the obtained analogs, Tyr-c[(R)-ß3-Lys-Phe-Phe-Asp]NH2 (RP-171) and Tyr-c[(S)-ß3-Lys-Phe-Phe-Asp]NH2, (RP-172), was investigated in vitro. Receptor radiolabeled displacement and functional calcium mobilization assays were performed to measure binding affinity and receptor activation of the new analogs. The obtained data revealed that only one of the diastereoisomeric peptides, RP-171, was able to selectively bind and activate MOR. Molecular modeling (docking and molecular dynamics (MD) simulations) suggests that both compounds should be accommodated in the MOR binding site. However, in the case of the inactive isomer RP-172, fewer hydrogen bonds, as well as instability of the canonical ionic interaction to Asp147, could explain its very low MOR affinity.

Real-Time Parallel-Serial LiDAR-Based Localization Algorithm with Centimeter Accuracy for GPS-Denied Environments.

In this paper, we introduce a real-time parallel-serial algorithm for autonomous robot positioning for GPS-denied, dark environments, such as caves and mine galleries. To achieve a good complexity-accuracy trade-off, we fuse data from light detection and ranging (LiDAR) and an inertial measurement unit (IMU). The proposed algorithm's main novelty is that, unlike in most algorithms, we apply an extended Kalman filter (EKF) to each LiDAR scan point and calculate the location relative to a triangular mesh. We also introduce three implementations of the algorithm: serial, parallel, and parallel-serial. The first implementation verifies the correctness of our innovative approach, but is too slow for real-time execution. The second approach implements a well-known parallel data fusion approach, but is still too slow for our application. The third and final implementation of the presented algorithm along with the state-of-the-art GPU data structures achieves real-time performance. According to our experimental findings, our algorithm outperforms the reference Gaussian mixture model (GMM) localization algorithm in terms of accuracy by a factor of two.

Identification of miRNA Biomarkers for Diverse Cancer Types Using Statistical Learning Methods at the Whole-Genome Scale.

Genome-wide analysis of miRNA molecules can reveal important information for understanding the biology of cancer. Typically, miRNAs are used as features in statistical learning methods in order to train learning models to predict cancer. This motivates us to propose a method that integrates clustering and classification techniques for diverse cancer types with survival analysis via regression to identify miRNAs that can potentially play a crucial role in the prediction of different types of tumors. Our method has two parts. The first part is a feature selection procedure, called the stochastic covariance evolutionary strategy with forward selection (SCES-FS), which is developed by integrating stochastic neighbor embedding (SNE), the covariance matrix adaptation evolutionary strategy (CMA-ES), and classifiers, with the primary objective of selecting biomarkers. SNE is used to reorder the features by performing an implicit clustering with highly correlated neighboring features. A subset of features is selected heuristically to perform multi-class classification for diverse cancer types. In the second part of our method, the most important features identified in the first part are used to perform survival analysis via Cox regression, primarily to examine the effectiveness of the selected features. For this purpose, we have analyzed next generation sequencing data from The Cancer Genome Atlas in form of miRNA expression of 1,707 samples of 10 different cancer types and 333 normal samples. The SCES-FS method is compared with well-known feature selection methods and it is found to perform better in multi-class classification for the 17 selected miRNAs, achieving an accuracy of 96%. Moreover, the biological significance of the selected miRNAs is demonstrated with the help of network analysis, expression analysis using hierarchical clustering, KEGG pathway analysis, GO enrichment analysis, and protein-protein interaction analysis. Overall, the results indicate that the 17 selected miRNAs are associated with many key cancer regulators, such as MYC, VEGFA, AKT1, CDKN1A, RHOA, and PTEN, through their targets. Therefore the selected miRNAs can be regarded as putative biomarkers for 10 types of cancer.

Antiproliferative effects of [D-Pro2, D-Trp7,9]-Substance P and aprepitant on several cancer cell lines and their selectivity in comparison to normal cells.

A neuropeptide, Substance P (SP), has mitogenic action in many types of cancer cells mediated via the neurokinin-1 receptor (NK1R). Small molecular NK1R antagonists have been frequently shown to possess anticancer activity both in vivo and in vitro, but there are only a few papers on such activity regarding peptide antagonists. In order to extend the data on this class of compounds, we have compared the effects of a peptide antagonist, [D-Pro2, D-Trp7,9]-Substance P, and a small molecular antagonist, aprepitant on the proliferation of five cancer and three normal cell lines. The comparison was based on three assays: cell proliferation test, MTT test and assay for colony formation. Consistently with earlier reports, aprepitant potently reduced cell proliferation in cancer cell lines in all assays, but in contrast to previous works, the compound was not selective and it affected normal cell lines to a similar degree. The studied peptide antagonist, [D-Pro2, D-Trp7,9]-Substance P, was able to decrease proliferation only in a few cell lines, and only in the highest concentration (100 µM). In a lower concentration, a slight pro-proliferative effect was observed in a few cell lines. No statistically significant effects on colony formation were found for this compound.