ABSTRACT
Navigating the complex landscape of high-dimensional omics data with machine learning models presents a significant challenge. The integration of biological domain knowledge into these models has shown promise in creating more meaningful stratifications of predictor variables, leading to algorithms that are both more accurate and generalizable. However, the wider availability of machine learning tools capable of incorporating such biological knowledge remains limited. Addressing this gap, we introduce BioM2, a novel R package designed for biologically informed multistage machine learning. BioM2 uniquely leverages biological information to effectively stratify and aggregate high-dimensional biological data in the context of machine learning. Demonstrating its utility with genome-wide DNA methylation and transcriptome-wide gene expression data, BioM2 has shown to enhance predictive performance, surpassing traditional machine learning models that operate without the integration of biological knowledge. A key feature of BioM2 is its ability to rank predictor variables within biological categories, specifically Gene Ontology pathways. This functionality not only aids in the interpretability of the results but also enables a subsequent modular network analysis of these variables, shedding light on the intricate systems-level biology underpinning the predictive outcome. We have proposed a biologically informed multistage machine learning framework termed BioM2 for phenotype prediction based on omics data. BioM2 has been incorporated into the BioM2 CRAN package (https://cran.r-project.org/web/packages/BioM2/index.html).
Subject(s)
Machine Learning , Phenotype , Humans , DNA Methylation , Algorithms , Computational Biology/methods , Software , Transcriptome , Genomics/methodsABSTRACT
In counter-current chromatography (CCC), linear scale-up is an ideal amplification strategy. However, when transferring from analytical to predictable preparative processes with high throughput, linear scale-up would be challenging due to limitations imposed by differences in instrument parameters, such as gravitational forces, tubing cross-section area, tubing length, column volume and flow rate. Some effective scale-up strategies have been studied for different instrument parameters, but so far, these scale-up works have only been tested on standard circular (SC) tubing. The previous research of our group found that rectangular horizontal (RH) tubing can double the separation efficiency compared with conventional SC tubing, and has industrial production potential. This paper used the separation of tilianin from Dracocephalum moldavica L. as an example to demonstrate how to scale up the optimized process from analytical SC tubing to preparative RH tubing. After systematic optimization of solvent systems, sample concentration and flow rate on the analytical CCC, the optimized parameters obtained were successfully transferred to the preparative CCC. The results showed that a crude sample of 2.07 g was successfully separated using a solvent system of n-hexane - ethyl acetate - ethanol - water (1:4:1:5, v/v/v/v) in reversed phase mode, and the three consecutive separations produced a total of 380 mg tilianin in 75 min with high purities of 98.3%, as analyzed by HPLC. The total throughput achieved from the analytical to semi-preparative scale was improved by 138 times (from 12 mg/h to 1.66 g/h), while the column volume was increased by only 46.5 times (from 15.5 mL to 720 mL). This is the successful application of CCC for the separation and purification of tilianin. Given that SC tubing is the traditional configuration for CCC columns, this study is a necessary step to prove the applicability of RH tubing columns for routine use and potential large-scale industrial applications.
Subject(s)
Countercurrent Distribution , Countercurrent Distribution/methods , Countercurrent Distribution/instrumentation , Glycosides/isolation & purification , Glycosides/analysis , Glycosides/chemistry , Pyrans/isolation & purification , Pyrans/analysis , Solvents/chemistry , Hexanes/chemistry , Lamiaceae/chemistry , Chromatography, High Pressure Liquid/instrumentation , Chromatography, High Pressure Liquid/methods , Ethanol/chemistry , Acetates/chemistry , FlavonoidsABSTRACT
Given the multifaceted biological functions of DNA-PK encompassing DNA repair pathways and beyond, coupled with the susceptibility of DNA-PK-deficient cells to DNA-damaging agents, significant strides have been made in the pursuit of clinical potential for DNA-PK inhibitors as synergistic adjuncts to chemo- or radiotherapy. Nevertheless, although substantial progress has been made with the discovery of potent inhibitors of DNA-PK, the clinical trial landscape requires even more potent and selective molecules. This necessitates further endeavors to expand the repertoire of clinically accessible DNA-PK inhibitors for the ultimate benefit of patients. Described herein are the obstacles that were encountered and the solutions that were found, which eventually led to the identification of compound 31t. This compound exhibited a remarkable combination of robust potency and exceptional selectivity along with favorable in vivo profiles as substantiated by pharmacokinetic studies in rats and pharmacodynamic assessments in H460, BT474, and A549 xenograft models.
Subject(s)
Antineoplastic Agents , Humans , Rats , Animals , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/pharmacokinetics , Cell Line, TumorABSTRACT
Onions are versatile and nutritious food widely used in various cuisines around the world. In our ongoing pursuit of bioactive substances with health benefits from red onion (Allium cepa L.) skin, a comprehensive chemical investigation was undertaken. Consequently, a total of 44 compounds, including three previously unidentified chalcones (1-3) were extracted from red onion skin. Of these isolates, chalcones 1-4 showed high affinity to A2A adenosine receptor (A2AAR), and chalcone 2 displayed the best binding affinity to A2AAR, with the IC50 value of 33.5 nM, good A2AAR selectivity against A1AR, A2BAR, and A3AR, and high potency in the cAMP functional assay (IC50 of 913.9 nM). Importantly, the IL-2 bioassay and the cell-mediated cytotoxicity assay demonstrated that chalcone 2 could boost T-cell activation. Furthermore, the binding mechanism of chalcone 2 with hA2AAR was elucidated by molecular docking. This work highlighted that the active chalcones in red onion might have the potential to be developed as A2AAR antagonists used in cancer immunotherapy.
ABSTRACT
ATM plays an important role in DNA damage response and is considered a potential target in cancer therapies. In this study, a goal-directed molecular generation approach based on ligand similarity and target specificity was applied to sample active molecules, and they were screened virtually to identify the theoretical lead compound 7a, which was later shown to inhibit ATM adequately. However, there is a main concern about its poor metabolic stability in vitro. Subsequent optimization was performed to improve the potency and selectivity toward ATM and attenuate the hepatic clearance in vitro, culminating in the identification of 10r with nanomolar ATM inhibition, excellent cellular sensitivity to radiation and chemotherapy drugs, and impressive pharmacokinetic profiles. Furthermore, 10r combined with irinotecan demonstrated a synergistic antitumor efficacy in SW620 xenograft models, suggesting that it could be a promising candidate drug combined with chemotherapy for the treatment of cancer.
Subject(s)
Neoplasms , Quinoxalines , Humans , Goals , Early Detection of Cancer , Irinotecan/pharmacology , Irinotecan/therapeutic use , Ataxia Telangiectasia Mutated Proteins/metabolismABSTRACT
Aralia elata is an important herb due to the abundance of pentacyclic triterpenoid saponins whose important precursors are squalene and OA. Here, we found that MeJA treatment promoted both precursors accumulation, especially the latter, in transgenic A. elata, overexpressing a squalene synthase gene from Panax notoginseng(PnSS). In this study, Rhizobium-mediated transformation was used to express the PnSS gene. Gene expression analysis and high-performance liquid chromatography (HPLC) were used to identify the effect of MeJA on squalene and OA accumulation. The PnSS gene was isolated and expressed in A. elata. Transgenic lines showed a very high expression of the PnSS gene and farnesyl diphosphate synthase gene (AeFPS) and a slightly higher squalene content than the wild-type, but endogenous squalene synthase (AeSS), squalene epoxidase (AeSE), and ß-amyrin synthase (Aeß-AS) gene were decreased as well as OA content. Following one day of MeJA treatment, the expression levels of PeSS, AeSS, and AeSE genes increased significantly. On day 3, the maximum content of both products reached 17.34 and 0.70 mg·g-1, which increased 1.39- and 4.90-fold than in the same lines without treatment. Transgenic lines expressing PnSS gene had a limited capability to promote squalene and OA accumulation. MeJA strongly activated their biosynthesis pathways, leading to enhance yield.
Subject(s)
Aralia , Oleanolic Acid , Squalene , Aralia/chemistry , Farnesyl-Diphosphate Farnesyltransferase/geneticsABSTRACT
Based on the pharmacological synergy of JAK2 and BRD4 in the NF-κB pathway and positive therapeutic effect of combination of JAK2 and BRD4 inhibitors in treating MPN and inflammation. A series of unique 9H-purine-2,6-diamine derivatives that selectively inhibited Janus kinase 2 (JAK2) and BRD4(BD2) were designed, prepared, and evaluated for their in vitro and in vivo potency. Among them, compound 9j exhibited acceptable inhibitory activity with IC50 values of 13 and 22 nM for BD2 of BRD4 and JAK2, respectively. The western blot assay demonstrated that 9j performed good functional potency in the NF-κB pathway and the phosphorylation of p65, IκB-α, and IKKα/ß signal intensities were suppressed on RAW264.7 cell lines. Furthermore, 9j significantly improved the disease symptoms in a Ba/F3-JAK2V617F allograft model. Meanwhile, 9j was also effective in relieving symptoms in an acute ulcerative colitis model. Taken together, 9j was a potent JAK2/BRD4(BD2) dual target inhibitor and could be a potential lead compound in treating myeloproliferative neoplasms and inflammatory diseases.
Subject(s)
Janus Kinase 2 , Myeloproliferative Disorders , Humans , Nuclear Proteins , NF-kappa B , Transcription Factors/metabolism , Myeloproliferative Disorders/drug therapy , Cell Cycle ProteinsABSTRACT
Counter-current chromatography (CCC) is a widely used liquid-liquid separation technique. Much work has been performed to improve the retention of stationary phases and throughput. In previous research, high aspect ratio rectangular horizontal (RH) tubing has been proven to be able to improve resolution and throughput in comparison with standard circular (SC) tubing. However, those modifications and improvements of tubing shapes have only been tested on analytical tubing thus far. This study aims to verify whether RH tubing could achieve similar high stationary phase retention (Sf) and throughput on a semi-preparative CCC apparatus. First, a lighter and larger volume semi-preparative bobbin with thin-wall RH tubing was successfully manufactured. Then the Sf of this bobbin was tested with n-hexane-ethyl acetate-methanol-water (HEMWat) and dichloromethane-methanol-water (DMW) solvent systems, and its maximum throughput was explored with the mixture of Magnolia officinalis Rehd. Et Wils. The results show that the thin-wall RH tubing bobbin can retain high Sf for these solvent systems, even at a relatively high mobile phase flow rate, which is consistent with the analytical bobbin results. The throughput test demonstrates that 2.12 × throughput can be obtained with the RH tubing column bobbin compared to the conventional SC tubing column bobbin without changing the outside dimensions of the bobbin. The present study is a necessary step for the application of the RH tubing bobbin from a laboratory analytical scale to preparative industrial scale.
Subject(s)
Countercurrent Distribution , Magnolia , Chromatography, High Pressure Liquid , Methanol , Solvents , WaterABSTRACT
We investigated the contamination levels of nine heavy metals (Mn, Pb, V, Cr, Co, Ni, Cu, Zn, and As) in 153 surface sediment samples collected along five tidal flats on the North Jiangsu coast, China. The spatial distributions of most heavy metals gradually decreased from the northern Sheyang region to the southern Jianggang region, while slightly increasing in the Rudong region. Principal component analysis indicated that Co, Ni, Cu, Zn, and As were mainly derived from the natural environment, V and Cr were mainly derived from human activities. Additionally, Mn and Pb influenced by both natural and human sources. The geo-accumulation index and the contamination factor indicated that heavy metal contamination in the sediments exhibited little to no pollution levels. The potential ecological risk index exhibiting low ecological risks. Meanwhile, the mean probable effect level quotient values indicating slight toxicity. Cr and Ni were the major contributors to toxicity.
Subject(s)
Metals, Heavy , Water Pollutants, Chemical , China , Environmental Monitoring , Geologic Sediments , Humans , Metals, Heavy/analysis , Risk Assessment , Water Pollutants, Chemical/analysisABSTRACT
Increased expression of glucose transporters, especially GLUT1 has been proven to be involved in the Warburg effect. Therefore, GLUT1-targeted oncological approaches are being successfully employed for clinical tumor diagnostic imaging (e.g. the 18F-FDG/PET), drug delivery and novel anticancer drug development. Despite the long history of the Warburg effect-targeted cancer diagnosis, other than antibody labeling, there have been no imaging tools developed for direct detection of the GLUT1 expression. Herein, we report the new strategy of using a non-antibody GLUT1 binding probe for Warburg effect-based tumor detection and diagnostic imaging. By specifically inhibits the transport function of GLUT1, the newly designed fluorescent probe, CUM-5, was found to be a useful tool not only for sensitive GLUT1-mediated cancer cell detection, but also for cell-based high-throughput GLUT inhibitor screening. In in vivo studies, CUM-5 shows clear advantages including desirable tumor-to-normal tissue contrast and excellent tumor selectivity (Tm/Bkg and Tm/Torg), as well as high fluorescence stability (long response time) and ideal physiological biocompatibility. In particular, the GLUT1 inhibitor probe offers the potential use for glycolysis-based diagnostic imaging in triple-negative breast cancer which is claimed to have unsatisfactory results with FDG/PET diagnosis, thus remaining a highly metastatic and lethal disease with a need for sensitive and precise identification.
Subject(s)
Neoplasms , Pharmaceutical Preparations , Cell Line, Tumor , Drug Evaluation, Preclinical , Early Detection of Cancer , Glucose Transporter Type 1 , Humans , Neoplasms/diagnostic imaging , Neoplasms/drug therapyABSTRACT
Oxaliplatin-based chemotherapy is the current standard of care in adjuvant therapy for advanced colorectal cancer (CRC). But acquired resistance to oxaliplatin eventually occurs and becoming a major cause of treatment failure. Thus, there is an unmet need for developing new chemical entities (NCE) as new therapeutic candidates to target chemotherapy-resistant CRC. Novel Pt(II) complexes were designed and synthesized as cationic monofunctional oxaliplatin derivatives for DNA platination-mediated tumor targeting. The complex Ph-glu-Oxa sharing the same chelating ligand of diaminocyclohexane (DACH) with oxaliplatin but is equally potent in inhibiting the proliferation of HT29 colon cancer cells and its oxaliplatin-resistant phenotype of HT29/Oxa. The in vivo therapeutic potential of Ph-glu-Oxa was confirmed in oxaliplatin-resistant xenograft model demonstrating the reversibility of the drug resistance by the new complex and the efficacy was associated with the unimpaired high intracellular drug accumulation in HT29/Oxa. Guanosine-5'-monophosphate (5'-GMP) reactivity, double-strand plasmid DNA cleavage, DNA-intercalated ethidium bromide (EB) fluorescence quenching and atomic force microscopy (AFM)-mediated DNA denaturing studies revealed that Ph-glu-Oxa was intrinsically active as DNA-targeting agent. The diminished susceptibility of the complex to glutathione (GSH)-mediated detoxification, which confers high intracellular accumulation of the drug molecule may play a key role in maintaining cytotoxicity and counteracting oxaliplatin drug resistance.
Subject(s)
Antineoplastic Agents/chemistry , Coordination Complexes/chemistry , Drug Resistance, Neoplasm/drug effects , Oxaliplatin/chemistry , Platinum/chemistry , Triazoles/chemistry , Animals , Antineoplastic Agents/metabolism , Antineoplastic Agents/pharmacology , Binding Sites , Cell Line, Tumor , Cell Survival/drug effects , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Coordination Complexes/metabolism , Coordination Complexes/pharmacology , DNA/chemistry , DNA/metabolism , Drug Design , Drug Screening Assays, Antitumor , Glutathione/chemistry , Humans , Mice , Mice, Nude , Molecular Dynamics Simulation , Nucleic Acid Conformation , Oxaliplatin/pharmacologyABSTRACT
Cubic boron nitride (cBN) is synthesized by a low-temperature solid state synthesis and in situ phase transformation route with NH(4)BF(4), B, NaBH(4) and KBH(4) as the boron sources and NaN(3) as the nitrogen source. Furthermore, two new strategies are developed, i.e., applying pressure on the reactants during the reaction process and introducing the structural induction effect. These results reveal that the relative contents of cBN are greatly increased by applying these new strategies. Finally, almost pure cBN (â¼90%) crystals are obtained by reacting NH(4)BF(4) and NaN(3) at 250 °C and 450 MPa for 24 h, with NaF as the structural induction material. The heterogeneous nucleation mechanism can commendably illuminate the structure induction effect of NaF with face center cubic structure. In addition, the induction effect results in the cBN nanocrystals presenting obvious oriented growth of {111} planes.