Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data.

With the increased use of gene expression profiling for personalized oncology, optimized RNA sequencing (RNA-seq) protocols and algorithms are necessary to provide comparable expression measurements between exome capture (EC)-based and poly-A RNA-seq. Here, we developed and optimized an EC-based protocol for processing formalin-fixed, paraffin-embedded samples and a machine-learning algorithm, Procrustes, to overcome batch effects across RNA-seq data obtained using different sample preparation protocols like EC-based or poly-A RNA-seq protocols. Applying Procrustes to samples processed using EC and poly-A RNA-seq protocols showed the expression of 61% of genes (N = 20,062) to correlate across both protocols (concordance correlation coefficient > 0.8, versus 26% before transformation by Procrustes), including 84% of cancer-specific and cancer microenvironment-related genes (versus 36% before applying Procrustes; N = 1,438). Benchmarking analyses also showed Procrustes to outperform other batch correction methods. Finally, we showed that Procrustes can project RNA-seq data for a single sample to a larger cohort of RNA-seq data. Future application of Procrustes will enable direct gene expression analysis for single tumor samples to support gene expression-based treatment decisions.

Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma.

BACKGROUND & AIMS: The complex tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) has hindered the development of reliable predictive biomarkers for targeted therapy and immunomodulatory strategies. A comprehensive characterization of the TME is necessary to advance precision therapeutics in PDAC. METHODS: A transcriptomic profiling platform for TME classification based on functional gene signatures was applied to 14 publicly available PDAC datasets (n = 1657) and validated in a clinically annotated independent cohort of patients with PDAC (n = 79). Four distinct subtypes were identified using unsupervised clustering and assessed to evaluate predictive and prognostic utility. RESULTS: TME classification using transcriptomic profiling identified 4 biologically distinct subtypes based on their TME immune composition: immune enriched (IE); immune enriched, fibrotic (IE/F); fibrotic (F); and immune depleted (D). The IE and IE/F subtypes demonstrated a more favorable prognosis and potential for response to immunotherapy compared with the F and D subtypes. Most lung metastases and liver metastases were subtypes IE and D, respectively, indicating the role of clonal phenotype and immune milieu in developing personalized therapeutic strategies. In addition, distinct TMEs with potential therapeutic implications were identified in treatment-naive primary tumors compared with tumors that underwent neoadjuvant therapy. CONCLUSIONS: This novel approach defines a distinct subgroup of PADC patients that may benefit from immunotherapeutic strategies based on their TME subtype and provides a framework to select patients for prospective clinical trials investigating precision immunotherapy in PDAC. Further, the predictive utility and real-world clinical applicability espoused by this transcriptomic-based TME classification approach will accelerate the advancement of precision medicine in PDAC.

Fabrication of 3D Oriented MOF Micropatterns with Anisotropic Fluorescent Properties.

Micropatterning crystalline materials with oriented pores is necessary for the fabrication of devices with anisotropic properties. Crystalline and porous metal-organic frameworks (MOFs) are ideal materials as their chemical and structural mutability enables precise tuning of functional properties for applications ranging from microelectronics to photonics. Herein, a patternable oriented MOF film is designed: by using a photomask under X-ray exposure, the MOF film decomposes in the irradiated areas, remaining intact in the unexposed regions. The MOF film acts simultaneously as a resist and as functional porous material. While the heteroepitaxial growth from aligned Cu(OH)2 nanobelts is used to deposit oriented MOF films, the sensitivity to radiation is achieved by integrating a brominated dicarboxylate ligand (Br2 BDC) into a copper-based MOF Cu2 L2 DABCO (DABCO = 1,4-diazabicyclo[2.2.2]octane; L = BDC/Br2 BDC). The lithographed samples act as diffraction gratings upon irradiation with a laser, thus confirming the quality of the extended MOF micropattern. Furthermore, the oriented MOF patterns are functionalized with fluorescent dyes. As a result, by rotating the polarization angle of the laser excitation, the alignment of the dye in the MOF is demonstrated. By controlling the functional response to light, this MOF patterning protocol can be used for the microfabrication of optical components for photonic devices.

Nanoporous Metal-Organic Framework Thin Films Prepared Directly from Gaseous Precursors by Atomic and Molecular Layer Deposition: Implications for Microelectronics.

Atomic/molecular layer deposition (ALD/MLD) allows for the direct gas-phase synthesis of crystalline metal-organic framework (MOF) thin films. Here, we show for the first time using krypton and methanol physisorption measurements that ALD/MLD-fabricated copper 1,4-benzenedicarboxylate (Cu-BDC) ultrathin films possess accessible porosity matching that of the corresponding bulk MOF.

Chemical Vapor Deposition and High-Resolution Patterning of a Highly Conductive Two-Dimensional Coordination Polymer Film.

Crystalline coordination polymers with high electrical conductivities and charge carrier mobilities might open new opportunities for electronic devices. However, current solvent-based synthesis methods hinder compatibility with microfabrication standards. Here, we describe a solvent-free chemical vapor deposition method to prepare high-quality films of the two-dimensional conjugated coordination polymer Cu-BHT (BHT = benzenehexanothiolate). This approach involves the conversion of a metal oxide precursor into Cu-BHT nanofilms with a controllable thickness (20-85 nm) and low roughness (<10 nm) through exposure to the vaporized organic linker. Moreover, the restricted metal ion mobility during the vapor-solid reaction enables high-resolution patterning via both bottom-up lithography, including the fabrication of micron-sized Hall bar and electrode patterns to accurately evaluate the conductivity and mobility values of the Cu-BHT films.

Vapor-Assisted Powder Synthesis and Oriented MOF-CVD Thin Films of the Metal-Organic Framework HKUST-1.

A vapor-assisted synthesis method was developed for the metal-organic framework (MOF) HKUST-1 in both powder and film format. The use of a solvent template supplied from the vapor phase is essential to form the framework under these conditions. Chemical vapor deposition of HKUST-1 films (MOF-CVD) results in smooth films that show the expected adsorption behavior. Interestingly, the HKUST-1 films obtained this way show a (111) preferred crystallographic orientation.

The Efficacy of Aprotinin Combinations with Selected Antiviral Drugs in Mouse Models of Influenza Pneumonia and Coronavirus Infection Caused by SARS-CoV-2.

The efficacy of aprotinin combinations with selected antiviral-drugs treatment of influenza virus and coronavirus (SARS-CoV-2) infection was studied in mice models of influenza pneumonia and COVID-19. The high efficacy of the combinations in reducing virus titer in lungs and body weight loss and in increasing the survival rate were demonstrated. This preclinical study can be considered a confirmatory step before introducing the combinations into clinical assessment.

Safety and efficacy of aviandr in patients with generalized anxiety disorder: A multicenter, randomized, double-blind, placebo-controlled, dose-finding, pilot study.

Generalized anxiety disorder (GAD) is associated with an imbalance in the functioning of the stimulating neurotransmitter systems in human's brain. We studied the safety and therapeutic efficacy of aviandr, the new noradrenergic and specific serotonergic antidepressant, for GAD patients in the phase II, double-blind, placebo-controlled, randomized, multicenter, pilot trial at 17 clinical sites of the Russian Federation. 129 eligible patients were 18 years and older and met the criteria for GAD diagnosis. The patients were randomly assigned (1:1:1) to receive oral aviandr at daily dose of 40 mg (cohort 1, n = 41) or 60 mg (cohort 2, n = 43) or placebo (cohort 3, n = 43) for 8 weeks. The patients were assessed by the Hamilton anxiety scale (HAM-A), Hamilton Depression Scale (HAM-D), Clinical Global Impression Scale (CGI-S), Visual Analogue Scale and vital signs. At week 8, the decreases of the HAM-A score were achieved in 53∙7%, 47∙7% and 16∙3% in cohorts 1, 2 and 3, respectively. Changes of HAM-A, HAM-D, CGI-S, and CGI-I scores in aviandr-treated patients were superior to placebo (p < 0∙001). The psychic components of anxiety decreased on the first day, throughout the 8 weeks of treatment and on a follow-up week after aviandr discontinuation. Aviandr (40 mg daily dose) reduced drowsiness compared to baseline, was safe, well-tolerated and did not cause serious or severe adverse events or signs of withdrawal syndrome within one week after treatment completion. Aviandr at both 40 and 60 mg daily doses demonstrated therapeutic efficacy in GAD patients over placebo.

Effect of Aprotinin and Avifavir® Combination Therapy for Moderate COVID-19 Patients.

COVID-19 is a contagious multisystem inflammatory disease caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We studied the efficacy of Aprotinin (nonspecific serine proteases inhibitor) in combination with Avifavir® or Hydroxychloroquine (HCQ) drugs, which are recommended by the Russian Ministry of Health for the treatment therapy of moderate COVID-19 patients. This prospective single-center study included participants with moderate COVID-19-related pneumonia, laboratory-confirmed SARS-CoV-2, and admitted to the hospitals. Patients received combinations of intravenous (IV) Aprotinin (1,000,000 KIU daily, 3 days) and HCQ (cohort 1), inhalation (inh) treatment with Aprotinin (625 KIU four times per day, 5 days) and HCQ (cohort 2) or IV Aprotinin (1,000,000 KIU daily for 5 days) and Avifavir (cohort 3). In cohorts 1-3, the combination therapy showed 100% efficacy in preventing the transfer of patients (n = 30) to the intensive care unit (ICU). The effect of the combination therapy in cohort 3 was the most prominent, and the median time to SARS-CoV-2 elimination was 3.5 days (IQR 3.0-4.0), normalization of the CRP concentration was 3.5 days (IQR 3-5), of the D-dimer concentration was 5 days (IQR 4 to 5); body temperature was 1 day (IQR 1-3), improvement in clinical status or discharge from the hospital was 5 days (IQR 5-5), and improvement in lung lesions of patients on 14 day was 100%.

Effect of different oxide and hybrid precursors on MOF-CVD of ZIF-8 films.

Chemical vapor deposition of metal-organic frameworks (MOF-CVD) will facilitate the integration of porous and crystalline coatings in electronic devices. In the two-step MOF-CVD process, a precursor layer is first deposited and subsequently converted to a MOF through exposure to linker vapor. We herein report the impact of different metal oxide and metalcone layers as precursors for zeolitic imidazolate framework ZIF-8 films.

Efficient delivery of oncolytic enterovirus by carrier cell line NK-92.

Many members of the enterovirus family are considered as promising oncolytic agents; however, their systemic administration is largely inefficient due to the rapid neutralization of the virus in the circulation and the barrier functions of the endothelium. We aimed to evaluate natural killer cells as carriers for the delivery of oncolytic enteroviruses, which would combine the effects of cell immunotherapy with virotherapy. We tested four strains of nonpathogenic enteroviruses against the glioblastoma cell line panel and evaluated the produced infectious titers. Next, we explored whether these virus strains could be delivered to the tumor by natural killer cell line NK-92, which is being actively evaluated as a clinically acceptable therapeutic. Several strains of enteroviruses demonstrated oncolytic properties, but only coxsackievirus A7 (CVA7) could replicate in NK-92 cells efficiently. We compared the delivery efficiency of CVA7 in vivo, using NK-92 cells and direct intravenous administration, and found significant advantages of cell delivery even after a single injection. This suggests that the NK-92 cell line can be utilized as a vehicle for the delivery of the oncolytic strain of CVA7, which would improve the clinical potential of this viral oncolytic for the treatment of glioblastoma multiforme and other forms of cancer.

Crystal structure of the non-steroidal anti-inflammatory drug (NSAID) tolmetin sodium.

The asymmetric unit of the title compound, sodium 2-[1-methyl-5-(4-methyl-benzo-yl)-1H-pyrrol-2-yl]acetate dihydrate, Na+·C15H14NO3 -·2H2O, contains two sodium cations, two organic anions (A and B) and two water mol-ecules. The coordination geometry around the sodium cations corresponds to a distorted octa-hedron. Each pair of sodium cations (A-A or B-B) is chelated by two bridging anions coordinated by the O atoms of the deprotonated carb-oxy-lic groups, and each sodium atom is coordinated by an O atom of a third anion, which connects pairs of sodium atoms, and a water mol-ecule. As a result, a two-dimensional polymer is formed in the crystal. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to analyze the inter-molecular contacts present in the crystal.

Synthesis, inhibitory activity and oral dosing formulation of AV5124, the structural analogue of influenza virus endonuclease inhibitor baloxavir.

BACKGROUND: The development and clinical implementation of the cap-dependent endonuclease (CEN) inhibitor baloxavir marboxil was a breakthrough in influenza therapy, but it was associated with the emergence of drug-resistant variants. OBJECTIVES: To design and synthesize structural analogues of CEN inhibitors and evaluate their safety, pharmacokinetics and antiviral potency in vitro and in vivo. METHODS: The drug candidate AV5124 and its active metabolite AV5116 were synthesized based on pharmacophore modelling. Stability in plasma and microsomes, plasma protein binding, cytotoxicity and antiviral activities were assessed in vitro. Pharmacokinetics after IV or oral administration were analysed in CD-1 mice. Acute toxicity and protective efficacy against lethal A(H1N1)pdm09 influenza virus challenge were examined in BALB/c mice. RESULTS: Pharmacophore model-assisted, 3D molecular docking predicted key supramolecular interactions of the metal-binding group and bulky hydrophobic group of AV5116 with the CEN binding site (Protein Data Bank code: 6FS6) that are essential for high antiviral activity. AV5116 inhibited influenza virus polymerase complexes in cell-free assays and replication of oseltamivir-susceptible and -resistant influenza A and B viruses at nanomolar concentrations. Notably, AV5116 was equipotent or more potent than baloxavir acid (BXA) against WT (I38-WT) viruses and viruses with reduced BXA susceptibility carrying an I38T polymerase acidic (PA) substitution. AV5116 exhibited low cytotoxicity in Madin-Darby canine kidney cells and lacked mitochondrial toxicity, resulting in favourable selective indices. Treatment with 20 or 50 mg/kg AV5124 prevented death in 60% and 100% of animals, respectively. CONCLUSIONS: Overall, AV5124 and A5116 are promising inhibitors of the influenza virus CEN and warrant further development as potent anti-influenza agents.

Template-Mediated Control over Polymorphism in the Vapor-Assisted Formation of Zeolitic Imidazolate Framework Powders and Films.

The landscape of possible polymorphs for some metal-organic frameworks (MOFs) can pose a challenge for controlling the outcome of their syntheses. Demonstrated here is the use of a template to control in the vapor-assisted formation of zeolitic imidazolate framework (ZIF) powders and thin films. Introducing a small amount of either ethanol or dimethylformamide vapor during the reaction between ZnO and 4,5-dichloroimidazole vapor results in the formation of the porous ZIF-71 phase, whereas other conditions lead to the formation of the dense ZIF-72 phase or amorphous materials. Time-resolved in situ small-angle X-ray scattering reveals that the porous phase is metastable and can be transformed into its dense polymorph. This transformation is avoided through the introduction of template vapor. The porosity of the resulting ZIF powders and films was studied by N2 and Kr physisorption, as well as positron annihilation lifetime spectroscopy. The templating principle was demonstrated for other members of the ZIF family as well, including the ZIF-7 series, ZIF-8_Cl, and ZIF-8_Br.

AVIFAVIR for Treatment of Patients With Moderate Coronavirus Disease 2019 (COVID-19): Interim Results of a Phase II/III Multicenter Randomized Clinical Trial.

In May 2020 the Russian Ministry of Health granted fast-track marketing authorization to RNA polymerase inhibitor AVIFAVIR (favipiravir) for the treatment of COVID-19 patients. In the pilot stage of Phase II/III clinical trial, AVIFAVIR enabled SARS-CoV-2 viral clearance in 62.5% of patients within 4 days, and was safe and well-tolerated. Clinical Trials Registration. NCT04434248.

Direct X-ray and electron-beam lithography of halogenated zeolitic imidazolate frameworks.

Metal-organic frameworks (MOFs) offer disruptive potential in micro- and optoelectronics because of the unique properties of these microporous materials. Nanoscale patterning is a fundamental step in the implementation of MOFs in miniaturized solid-state devices. Conventional MOF patterning methods suffer from low resolution and poorly defined pattern edges. Here, we demonstrate the resist-free, direct X-ray and electron-beam lithography of MOFs. This process avoids etching damage and contamination and leaves the porosity and crystallinity of the patterned MOFs intact. The resulting high-quality patterns have excellent sub-50-nm resolution, and approach the mesopore regime. The compatibility of X-ray and electron-beam lithography with existing micro- and nanofabrication processes will facilitate the integration of MOFs in miniaturized devices.

Synthesis, biological evaluation and in silico modeling of novel pan-genotypic NS5A inhibitors.

A series of novel small-molecule pan-genotypic hepatitis C virus (HCV) NS5A inhibitors with picomolar activity containing 2-[(2S)-pyrrolidin-2-yl]-5-[4-(4-{2-[(2S)-pyrrolidin-2-yl]-1H-imidazol-5-yl}buta-1,3-diyn-1-yl)phenyl]-1H-imidazole core was designed based on molecular modeling study and SAR analysis. The constructed in silico model and docking study provide a deep insight into the binding mode of this type of NS5A inhibitors. Based on the predicted binding interface we have prioritized the most crucial diversity points responsible for improving antiviral activity. The synthesized molecules were tested in a cell-based assay, and compound 1.12 showed an EC50 value in the range of 2.9-34 pM against six genotypes of NS5A HCV, including gT3a, and demonstrated favorable pharmacokinetic profile in rats. This lead compound can be considered as an attractive candidate for further clinical evaluation.

(1R,3S)-3-(1H-Benzo[d]imidazol-2-yl)-1,2,2-tri-methyl-cyclo-pentane-1-carb-oxy-lic acid as a new anti-diabetic active pharmaceutical ingredient.

The chiral title compound, C16H20N2O2, which can be used for producing active pharmaceutical ingredients for treatment of type 2 pancreatic diabetes and other pathologies dependent on insulin resistance, was prepared from (1R,3S)-camphoric acid and o-phenyl-enedi-amine. It crystallized from an ethanol solution in the chiral monoclinic P21 space group. The five-membered ring adopts a twisted conformation with the methyl-substituted C atoms displaced by -0.273 (5) and 0.407 (5) Šfrom the mean plane through the other three atoms. In the crystal, mol-ecules are linked by O-H⋯N hydrogen bonds, forming chains along the a-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to analyze the inter-molecular contacts present in the crystal.

Methylation of Methyl 4-Hydroxy-2-thioxo-1,2-dihydroquinoline-3-carboxylate: Synthetic, Crystallographic, and Molecular Docking Studies.

Consecutive alkylation of 4-hydroxy-2-thioxo-1,2-dihydroquinoline-3-carboxylate by CH3I has been investigated to establish regioselectivity of the reaction for reliable design and synthesis of combinatorial libraries. In the first stage, the product of S-methylation-methyl 4-hydroxy-2-(methylthio)quinoline-3-carboxylate was obtained. The subsequent alkylation with CH3I led to the formation of both O- and N-methylation products mixture-methyl 4-methoxy-2-(methylthio)quinoline-3-carboxylate and methyl 1-methyl-2-(methylthio)-4-oxo-1,4-dihydroquinoline-3-carboxylate with a predominance of O-methylated product. The structure of synthesized compounds was confirmed by means of elemental analysis, 1H-NMR, 13C-NMR, LC/MS, and single-crystal X-ray diffraction. The quantum chemical calculations of geometry and electron structure of methyl 4-hydroxy-2-(methylthio)quinoline-3-carboxylate's anion were carried out. According to molecular docking simulations, the studied compounds can be considered as potent inhibitors of Hepatitis B Virus replication. Experimental in vitro biological studies confirmed that studied compounds demonstrated high inhibition of HBV replication in 10 µM concentration.

Non-rigid Diarylmethyl Analogs of Baloxavir as Cap-Dependent Endonuclease Inhibitors of Influenza Viruses.

4-Substituted 2,4-dioxobutanoic acids inhibit influenza virus cap-dependent endonuclease (CEN) activity. Baloxavir marboxil, 4, is approved for treating influenza virus infections. We describe here the synthesis and biological evaluation of active compounds, 5a-5g, and their precursors (6a, 6b, 6d, and 6e) with flexible bulky hydrophobic groups instead of the rigid polyheterocyclic moieties. In silico docking confirmed the ability of 5a-5g to bind to the active site of influenza A CEN (PDB code: 6FS6) like baloxavir acid, 3. These novel compounds inhibited polymerase complex activity, inhibited virus replication in cells, prevented death in a lethal influenza A virus mouse challenge model, and dramatically lowered viral lung titers. 5a and 5e potently inhibited different influenza genera in vitro. Precursors 6a and 6d demonstrated impressive mouse oral bioavailability with 6a, providing effective in vivo protection. Thus, these novel compounds are potent CEN inhibitors with in vitro and in vivo activity comparable to baloxavir.