Combinatorial Chemistry & High Throughput Screening - Volume 26, Issue 6, 2023

Background: Aptamers, consisting of single-stranded DNA or RNA, have secondary and tertiary structures which could bind specifically to target molecules. They are characterized by strong specificity, high affinity, low molecular weight, and low immunogenicity; therefore, the current research focuses on their potential as a targeted drug carrier, a diagnostic probe for diseases, or as a direct therapeutic drug. Objective: In this review, how to improve the success rate of adaptor screening and the optimization after screening is described. Results: For aptamer screening, an efficient selection strategy is needed. In this article, by analyzing key aspects of SELEX such as initial library design, screening procedures, truncation and modification after screening, a comprehensive analysis of each step that might meet obstacles in SELEX is provided. Conclusion: Aptamers, which possess the specificity and affinity with the target, can serve as targeted drug carriers or biosensors for diagnosing a disease. If the problems in the screening process in cell-SELEX technology, truncation, and modification after screening are solved, it will have a broader range of applications.

Background: Highland barley Monascus purpureus Went, a traditional Tibetan medicine with food functions, which is fermented by Monascus purpureus with highland barley as substrate. It possesses various medical functions of promoting blood circulation and removing blood stasis, invigorating spleen and promoting digestion in folk of the Qinghai-Tibet Plateau in China. This review provides a comprehensive overview of ethnopharmacology, phytochemistry, and pharmacology of highland barley Monascus purpureus Went. Methods: The references of highland barley Monascus purpureus Went were retrieved from the online database, such as Web of Science, Google Scholar, SciFinder, PubMed, SpringLink, Elsevier, Willy, CNKI, and so on. Results: Phytochemical research revealed that highland barley Monascus purpureus Went contained multiple chemical components, including Monascus pigments, monacolins, lactones, and other compounds. The reported pharmacological activities of highland barley Monascus purpureus Went included hypolipidemic, anti-nonalcoholic fatty liver disease, and hepatoprotective activities. Conclusion: In a word, botany, ethnopharmacology, phytochemistry and pharmacology of highland barley Monascus purpureus Went were reviewed comprehensively in this paper. In the future, highland barley Monascus purpureus Went needs further study, such as paying more attention to quality control and utilization of medicine. Therefore, this review may provide a theoretical basis and valuable data for future studies and exploitations on highland barley Monascus purpureus Went.

The Epidermal Growth Factor Receptor (EGFR) activation appears essential in tumor growth and progression. Targeting EGFR signaling pathway has become an exciting area in cancer therapy. Synthetic chemotherapy drugs have been used to inhibit some EGFR signaling in various cancer cells. The use of naturally occurring compounds as EGFR inhibitors is an attractive area for research due to the urgent need to combat resistance over current EGFR inhibitors. In this review, we first summarize the schematic role of EGFR in cancer and the current EGFR inhibitor used, its advantage, and disadvantage. Next, we discuss the natural products that have been reported as the source of EGFR inhibitors. The discussion covers the natural products which where majorly reported from the year 2005-2020. A total of 21 groups of natural compounds and their derivatives were reported to have the potential to inhibit EGFR signaling pathways. We then discuss the advanced technologies and approaches that rapidly discover EGFR inhibitor-based natural products. Hopefully, this literature review could increase the excitement of finding an effective EGFR pathway inhibitor from natural products.

Background: L-proline is a natural amino acid having secondary amine functionality and acts as a bifunctional catalyst (organo-catalyst). The amino-functional group acts as Lewis base type while carboxylic acids act as Brønsted acid type catalysts. It catalyzed different asymmetric syntheses, including known reactions such as Aldol condensation, Mannich reaction, Michael Addition, Knoevenagel condensation, Hantzsch synthesis, OXA-Michael Henry tandem, Ullmann reactions, Wieland-Miescher ketone synthesis, Robinson annulation, Biginelli reaction, α- amination. It is also an essential catalyst for synthesizing heterocyclic skeletons such as coumarin, spiro-oxindoles, imidazoles, benzimidazoles, quinoxalines, podophyllotoxin, benzothiazoles, isoxazolidines, phenothiazines, aziridine, indole, 1,5-benzodiazepines, pyridine, and quinazolines. Objective: In this review, we had the objective to critically summarize the use of proline and proline derivatives as catalysts of multicomponent reactions performed in various media and leading to synthetically and biologically relevant heterocycles, a very important class of compounds that constitutes over 60% of drugs and agrochemicals. Methods: All scholarly articles for L-Proline catalyzed reactions were retrieved from ScienceDirect, Google Scholar , PubMed, etc. Results and Conclusion: Given the importance of L-Proline based reactions, it has been observed to have tremendous applications in organic chemistry. It can also act as a 'Green catalyst'.

Ferroptosis is an iron-dependent, nonapoptotic form of regulatory death and has received extensive attention. Fenton reaction related to iron metabolism release high levels of Reactive Oxygen Species (ROS), and the intracellular ROS content is closely related to various diseases; the iron ion concentration in many diseased cells is also disordered. In this paper, the advances in ferroptosis research are summarized, and the regulatory mechanisms of ferroptosis, including inducers and regulatory protein of ferroptosis in cancer progression. We expect that this study will benefit the further development of basic research and clinical application of ferroptosis for cancer treatment.

Background: Cross-linked porous carbon nanofibers (CNF) were successfully prepared by electrospinning and high-temperature carbonization. Polyacrylonitrile (PAN) as the carbon source and genipin as the cross-linking agent were used to prepare cross-linked porous carbon nanofibers (CNF). Materials and Methods: The field emission scanning electron microscopy (SEM), transmission electron microscope (TEM), automatic specific surface and porosity analyzer Brunner Emmet Teller (BET), X-ray diffraction (XRD), and a laser confocal microspectroscope (Raman, XploRA PLUS, Horiba) were used to characterize the materials. The CNF suspension was dropped on the surface of the bare glassy carbon electrode by the drip coating method to obtain a CNF-modified electrode. Cyclic voltammetry was used to study the electrochemiluminescence behavior of difenidol hydrochloride on CNF-modified glassy carbon electrode (Glassy Carbon Electrode, GCE). Results and Discussion: Herein, we synthesised a kind of crosslinked carbon nanofibers and designed a novel ECL biosensor. Under the optimal conditions, the concentration of difenidol hydrochloride exhibited a linear relationship with the peak current in the range of 8.0×10^-8 to 1.0×10^-4 mol/L, with the correlation coefficient of R²=0.997, and a low detection limit (1.2×10^-8 mol/L). Difenidol hydrochloride in difenidol hydrochloride tablets was tested, and the recovery rate of sample addition was estimated to be 83.17%-92.17%, and the RSD value to be <5.0%. The designed platform exhibited excellent analytical performance for difenidol hydrochloride determination.

Objective: To explore the clinical efficacy of Zhuang Medicine Lotus Acupuncture Cupping Stasis Therapy on patients with postherpetic neuralgia (PHN) and its action mechanism. Methods: 36 patients are randomly divided into Lotus Acupuncture Cupping Stasis Therapy group, pure cupping group and gabapentin group, with a total of five observation points for the first, fifth, tenth, fifteenth, and twentieth sessions of therapy (one session every three days). At each observation point, the venous blood of the patients is taken, and the contents of and changes in WNT3a, Frizzled8, β-catenin, IL-18, TNF-α, NR2B, NK-1 and SP are tested by ELISA, RT-PCR and WesternBlot, respectively. The VAS scores and safety of the patients in the three groups are compared. Results: With increased time spent in therapy, the VAS scores of patients in each group decreased gradually and there was a significant reduction in pain in patients in the Lotus Acupuncture Cupping Stasis Therapy group compared to the gabapentin and pure cupping groups (P<0.05). The levels of IL-18, TNF-α, NK-1, SP, WNT3a, Frizzled 8 and β-catenin in the serum of all patients experienced a constant decline over time (P<0.05); the levels of the aforesaid factors in the serum of patients in the Lotus Acupuncture Cupping Stasis Therapy group dropped remarkably after the tenth session of therapy compared to those in gabapentin and pure cupping groups (P<0.05). Conclusions: Zhuang Medicine Lotus Acupuncture Cupping Stasis Therapy can significantly reduce the pain of PHN patients, with a good therapeutic effect, and it is worthy of clinical use.

Background: Premature ovarian failure is a heterogeneous disease that severely affects the quality of life of women in their reproductive years. The ancient classical Chinese medicine compounds Zuo Gui Wan and You Gui Wan have great potential to treat premature ovarian failure, but the similarities and differences in their pharmacological mechanisms for treating POF are not yet clear. Methods: In this study, the public database was used to screen the active ingredients and potential targets of Zuo Gui Wan and You Gui Wan. The similarities and differences in the potential targets of both pills for the treatment of POF were analysed using the POF-related genes obtained from OMIM and GeneCards. The protein-protein interaction network was established and collated to form a drug-active ingredient-target gene network using STRING. Finally, the drug-target-pathway network was constructed by enrichment analysis to find the differences in target enrichment on the same pathway. Results: Pharmacological analysis of the network showed that Zuo Gui Wan contains 72 active ingredients, while You Gui Wan has 112. A total of 62 common compositions, such as quercetin and kaempferol, were identified. Amongst them were 10 unique compounds, such as hydroxyproline and cholesterol, in Zuo Gui Wan and 50 exclusive compounds, such as Karanjin and betacarotene, in You Gui Wan. In addition, 14 overlapping targets, including MAPK1, CXCL8, TNF, IL6, and EGFR, were determined amongst the first 20 targets in the treatment of POF by both pills, demonstrating that the core mechanism of POF treatment is similar between the two. Pathway enrichment analysis showed 87 identical and significant pathways between Zuo Gui Wan and You Gui Wan, including IL-17, TNF, PI3K-Akt, oestrogen, VEGF, and other pathways. Zuo Gui Wan has 12 special pathways, such as natural killer cell-mediated cytotoxicity and intestinal immune network for IgA production. You Gui Wan has nine unique pathways, such as insulin secretion and glucagon signalling pathway. Conclusion: Zuo Gui Wan and You Gui Wan could treat POF by inhibiting oxidative stress and inflammation, regulating hormone levels, improving ovarian function, and promoting follicular development. Zuo Gui Wan is inclined to immune regulation, while You Gui Wan prefers insulin regulation. Therefore, similarities and differences clearly exist in the specific mechanisms of Zuo Gui Wan and You Gui Wan in the treatment of POF.

Background: This study aimed to determine the features and differentiation of Giant Cell Reparative Granuloma (GCRG) and Giant Cell Tumor (GCT) of the head on CT and MRI. Methods: This retrospective study included six patients with histopathology-confirmed head GCRG and 5 patients with histopathology-confirmed head GCT. All images were independently reviewed by two radiologists. The growth pattern, bone changes, MRI signal intensity, enhancement patterns and other image features were recorded. All patients received CT scans and MR images. Results: All the lesions were located centrally in the bone. Osteolytic bone destruction and expansive growth patterns were observed on CT images. Four of six cases broke the cortical bone with residual cortical bone, and the last two showed a thin cortex in GCRG. Five cases broke the cortical bone with residual cortical bone in GCT. There were enhancing septations in GCT lesions on contrast- enhanced T1-Weighted Images (T1WI) while enhancing septations were not present in GCRG cases. The size of GCT lesions was larger than that of GRCG. GCRG and GCT showed iso-low signals on T1WI and iso-high signals on T2-Weighted Images (T2WI). There was a case with cystic or necrotic lesions in each of the two types of lesions. Osteolytic bone destruction and expansive growth patterns were observed in GCTs and GCRGs. Conclusion: The size of the GRCG lesion was smaller than that of the GCT. The presence of enhancing septations and the size of the lesion may distinguish GCTs from GCRG.

Background: Necrotizing enterocolitis (NEC) is a neonatal intestinal necrotizing disease caused by various factors in newborns. Sulforaphane (SFN) has a strong anti-inflammatory ability and a certain protective effect on intestinal diseases. Objective: NEC is a common developed gastrointestinal exigency in an untimely baby. SFN is a naturally originated isothiocyanate that has beneficial effects on the intestinal system.The purpose of this study is to study the protective effect of SFN on endoplasmic reticulum stress (ERS)-related NEC. Methods: The newborn mice were randomly divided into control (n = 15), NEC (n = 20), and NEC+SFN (n = 18) groups. Mice in NEC and SFN+NEC groups were injected with 0.1 μl normal saline or 20 mg/kg/d SFN, respectively. After that, the weight and survival of the mice were recorded every day. Then the mice were sacrificed after 96 h of modeling; ileum tissue and blood samples were collected for qPCR, Western blot, ELISA, HE staining, TUNEL staining, and immunohistochemistry assays. Results: SFN significantly inhibited the mRNA expression of BIP, CHOP, IL-1β and IL-6, and protein expression of Bax, Caspase-3, Caspase-9 and CHOP, and promoted the expression of Bcl-2 in ER-induced NEC mice intestinal tissues (P<0.01). Meanwhile, SFN could suppress the serum levels of IL-8, IL-10, IL-6, TNF-α, and IL-1β, and positive expression of TLR4 and NF-ΚB (P<0.01), and promote the serum levels of IL-10. HE staining showed that SFN alleviated the NEC intestinal tissue injury, and TUNNEL staining showed that SFN could reduce the rate of NEC apoptotic cells (P<0.01). Moreover, SFN treatment improved the body weight and survival rate in NEC mice. Conclusion: SFN could effectively protect against ERS-induced inflammation and apoptosis in NEC mice.

Background: SARS-CoV-2 emerged in late 2019 and caused COVID-19. Patients treated with Zyesami were found to have a 3-fold decrease in respiratory failure and improved clinical outcomes. It was reported that Zyesami inhibits RNA replication of SARS-CoV-2, including several non-structural proteins essential in viral RNA replication. SARS-CoV-2 is a distinctive virus that requires nsp10 and nsp16 for its methyltransferases activity which is crucial for RNA stability and protein synthesis. Objective: We aimed the in silico determination of inhibitory consequences of Zyesami on the SARS-CoV-2 nsp10/nsp16 complex. Targeting SARS-CoV-2 nsp10/ nsp16 protein complex may be used to develop a drug against COVID-19. Methods: I-TASSER was used for secondary structure prediction of Zyesami. CABS-dock was used to model Zyesami with SARS-CoV-2 nsp16 interaction. The docked complex was visualized using PyMol. The quality of the docking model was checked by using ProQdock. Results: The 3D structure of SARS-CoV 2, nsp10/nsp16 showed that essential interactions exist between nsp10 and nsp16. Significant contact areas of Zyesami exist across amino acid residues of nsp10; Asn⁴⁰-Thr⁴⁷, Val57-Pro⁵⁹, Gly⁶⁹-Ser⁷², Cys⁷⁷-Pro⁸⁴, Lys⁹³-Tyr⁹⁶. In addition, polar contacts between nsp16 and Zyesami are Asn²⁹⁹-Ser⁴⁴⁰, Val²⁹⁷-Asn⁴⁴³, Gly¹⁴⁹-Tyr⁴³⁷, Gln¹⁵⁹-Lys⁴³⁰, Asn¹⁷⁸- Arg⁴²⁹, Ser¹⁴⁶-Arg⁴²⁹, Ser¹⁴⁶-Arg⁴²⁹, Lys¹⁴⁷-Arg⁴²⁹, Asr²²¹-Thr⁴²², Lys¹⁸³-Asp⁴²³, Lys¹⁸³-Asp⁴²³, and Gln²¹⁹-Asp⁴²³ the residues are shown of nsp16 and Zyesami respectively. Conclusion: The structural bioinformatics analyses have indicated the potential binding specificity of Zyesami and nsp16. Data predict how the initial binding of Zyesami with nsp10 and nsp16 may occur. Moreover, this binding could significantly inhibit the 2 -O-MTase activity of the SARSCoV nsp10/16 complex.

Aims and Objective: The lack of effective treatments for myocardial ischemiareperfusion (MI-R) injury severely restricts the effectiveness of the treatment of ischemic heart disease. In the present research, we aimed to investigate the protective effect and molecular mechanism of penehyclidine hydrochloride (PHC) on MI-R cells. Methods: Cell viability was quantified using CCK8. Cell apoptosis was analyzed using flow cytometry. Western blot and Elisa assays were used for the detection of target proteins. Results: PHC pretreatment attenuated the inhibition of cell viability and decreased the percentage of apoptosis induced by simulated ischemia reperfusion (SIR). Platelet-derived growth factor B (PDGF-B) and its downstream AKT pathway were activated in PHC pretreated cells. After siRNAPDGF- B transfection, cell viability was inhibited and apoptosis was activated in PHC pretreated SIR cells, suggesting that PHC protected cells from SIR. PDGF-B knockdown also increased the levels of CK, LDH, IL-6 and TNF-α in PHC pretreated SIR cells. The effect of AKT inhibitor on H9C2 cells was consistent with that of PDGF-B knockdown. Conclusion: PHC pretreatment can protect cardiomyocytes from the decrease of cell activity and the increase of apoptosis caused by reperfusion through up-regulating PDGF-B to activate PI3K pathway. Our study indicates that PHC is a potential drug to protect cells from reperfusion injury and PDGF-B is a potential target for preventing MI-R injury.

Background: P38α, emerging as a hot spot for drug discovery, is a member of the mitogen- activated protein kinase (MAPK) family and plays a crucial role in regulating the production of inflammatory mediators. However, despite a massive number of highly potent molecules being reported and several under clinical trials, no p38α inhibitor has been approved yet. There is still demand to discover novel p38α to deal with the safety issue induced by off-target effects. Objective: In this study, we performed a machine learning-based virtual screening to identify p38α inhibitors from a natural products library, expecting to find novel drug lead scaffolds. Methods: Firstly, the training dataset was processed with similarity screening to fit the chemical space of the natural products library. Then, six classifiers were constructed by combing two sets of molecular features with three different machine learning algorithms. After model evaluation, the three best classifiers were used for virtual screening. Results: Among the 15 compounds selected for experimental validation, picrasidine S was identified as a p38α inhibitor with the IC50 as 34.14 μM. Molecular docking was performed to predict the interaction mode of picrasidine S and p38α, indicating a specific hydrogen bond with Met109. Conclusion: This work provides a protocol and example for machine learning-assisted discovery of p38α inhibitor from natural products, as well as a novel lead scaffold represented by picrasidine S for further optimization and investigation.

Background: Radix Paeoniae Alba is a traditional Chinese herbal medicine. It can accelerate salivary secretion and alleviate the dry mouth of patients with Sjogren’s syndrome (SS). Although it is widely used in clinical treatment, its target and mechanism remain unclear. Objective: This study aims to analyze the main components of Radix Paeoniae Alba, explore the target genes, and propose the possible mechanism for Radix Paeoniae Alba’s acceleration of salivary secretion. Methods: The main active components and potential targets of Radix Paeoniae Alba were searched through the TCMSP database. Efforts were made to search for the related genes of Sjogren’s syndrome in OMIM and GeneCards databases. Cytoscape v3.8.0 software was used to link target genes of active components and key genes of the disease. The software Autodock vina1.1.2. was adopted to simulate the interaction between active components and target genes. Human submandibular gland (HSG) cells were used in vitro experiments to verify the results of our analysis. Results: β-Sitosterol, the main component of Radix Paeoniae Alba, may intervene in the disease through CHRM3. Molecular docking shows β-Sitosterol has a high affinity with CHRM3, and the interaction between CHRM3 and β-Sitosterol is the basis of biological activity. The in vitro experiments showed that β-Sitosterol could significantly up-regulate the mRNA and protein expression levels of both CHRM3 and secretion-related genes in HSG cells. Conclusion: Our study shows that the chemical components of Radix Paeoniae Alba have a positive effect on the related mechanism of salivary secretion. We found that β-Sitosterol can promote the expression of CHRM3, stimulate salivary secretion, treat Sjogren’s syndrome and potentially improve its prognosis.

Background: Experimental studies have shown that curcumin exerts neuroprotective effects in animal models with middle cerebral artery occlusion (MCAO). However, the mechanisms of protective effects of curcumin in MCAO are not fully understood. Objective: This study aims to investigate the key neurogenesis targets of curcumin action in mouse brain with MCAO. Methods: The MCAO models were established in mice. High-throughput sequencing was used to identify differentially expressed mRNA, lncRNA, and circRNA. The reverse expressed mRNAs, lncRNA, and circRNA in sham vs. MCAO and MCAO vs. curcumin were identified. Biological functions were determined by gene ontology (GO) analyses. The protein-protein interaction (PPI) network of neurogenesis-related genes was constructed. Next, neurogenesis-related lncRNA/ circRNA-miRNA-mRNA ceRNA networks were constructed. Results: The total of reverse expressed 1215 mRNAs, 32 lncRNAs, and 43 circRNAs were filtered based on the 2 series (sham vs. MCAO and MCAO vs. Curcumin). The functional enrichment analysis of 1215 reverse expressed mRNAs found that they were involved in neurogenesis, neuron generation, neurogenesis regulation, and others. The PPI network of neurogenesis-related genes consisted of 115 nodes, including 27 down-regulated genes and 36 up-regulated genes. Furthermore, the neurogenesis-related lncRNA/circRNA-miRNA-mRNA ceRNAs networks were constructed, and 5 lncRNA ceRNA networks and 3 circRNA ceRNA networks were explored. Conclusion: Our study revealed that curcumin exerts neuroprotective effects by regulating neurogenesis. The neurogenesis-related lncRNA/circRNA-miRNA-mRNA ceRNA networks are potential therapeutic targets of curcumin in MCAO. This study provided a theoretical basis for curcumin exerting neuroprotective effects in MCAO.

Background: A new strain of a novel disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been recently declared a pandemic by the World Health Organization (WHO). The virus results in significant mortality and morbidity across the planet; therefore, novel treatments are urgently required. Recently deposited crystallographic structures of SARS-CoV-2 proteins have ignited the interest in virtual screenings of large databases. Objective: In the current study, we evaluated the inhibitory capacity of the IMPPAT phytochemical database (8500 compounds) and the SuperDRUG2 dataset (4000 compounds) in SARS-CoV-2 main protease and helicase Nsp13 through consensus-based docking simulations. Methods: Glide and GOLD 5.3 were implemented in the in silico process. Further MM/GBSA calculations of the top 10 inhibitors in each protein were carried out to investigate the binding free energy of the complexes. An analysis of the major ligand-protein interactions was also conducted. Results: After the docking simulations, we acquired 10 prominent phytochemicals and 10 FDAapproved drugs capable of inhibiting Nsp5 and Nsp13. Delphinidin 3,5,3'-triglucoside and hirsutidin 3-O-(6-O-p-coumaroyl)glucoside demonstrated the most favorable binding free energies against Nsp5 and Nsp13, respectively. Conclusion: In conclusion, the analysis of the results identified that the phytochemicals demonstrated enhanced binding capacities compared to the FDA-approved database.