Histopathological subtyping of high-grade serous ovarian cancer using whole slide imaging

OBJECTIVE

We have established 4 histopathologic subtyping of high-grade serous ovarian cancer (HGSOC) and reported that the mesenchymal transition (MT) type has a worse prognosis than the other subtypes. In this study, we modified the histopathologic subtyping algorithm to achieve high interobserver agreement in whole slide imaging (WSI) and to characterize the tumor biology of MT type for treatment individualization.

METHODS

Four observers performed histopathological subtyping using WSI of HGSOC in The Cancer Genome Atlas data. As a validation set, cases from Kindai and Kyoto Universities were independently evaluated by the 4 observers to determine concordance rates. In addition, genes highly expressed in MT type were examined by gene ontology term analysis. Immunohistochemistry was also performed to validate the pathway analysis.

RESULTS

After algorithm modification, the kappa coefficient, which indicates interobserver agreement, was greater than 0.5 (moderate agreement) for the 4 classifications and greater than 0.7 (substantial agreement) for the 2 classifications (MT vs. non-MT). Gene expression analysis showed that gene ontology terms related to angiogenesis and immune response were enriched in the genes highly expressed in the MT type. CD31 positive microvessel density was higher in the MT type compared to the non-MT type, and tumor groups with high infiltration of CD8/CD103 positive immune cells were observed in the MT type.

CONCLUSION

We developed an algorithm for reproducible histopathologic subtyping classification of HGSOC using WSI. The results of this study may be useful for treatment individualization of HGSOC, including angiogenesis inhibitors and immunotherapy.

In vitro antioxidant, anti-inflammatory, and anticancer activities of mixture Thai medicinal plants

BACKGROUND

The phytochemical study of medicinal plants is rapidly gaining popularity with many pharmacologic effects. This study aims to determine the antioxidant capacity as well as anticancer and antimigration activities of Clear belongs Plus extract (CBL-P) which consisted of five medicinal plants namely, Alpinia galanga, Piper nigrum, Citrus aurantifolia, Tiliacora triandra, and Cannabis sativa on human colon cancer cells SW620 and HCT116 cell lines, and human non-small cell lung cancer cells A549 and NCI-H460 cell lines.

METHODS

In this study the dried-plant powder was extracted using 90% ethanol. Additionally, CBL-P was studied antioxidative activity via DPPH and ABTS assays and anti-inflammatory activities using nitric oxide assay using Griess reaction. Antiproliferation and antimigration of CBL-P were investigated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) and scratch assay.

RESULTS

The results showed that CBL-P had potent antiproliferative activity with IC₅₀ values in a concentration- and time-dependent manners for all four cell lines. CBL-P also possessed potent antimigration activity against all studied cancer cells. CBL-P demonstrated antimigration activity on four different types of cancer cells (A549, NCI-H460, HCT116, and SW620) after 48 h of incubation, with the greatest effect seen at the highest concentration tested (15 μg/mL) in A549 cells (10.23% of wound closure) and NCI-H460 cells (9.16% of wound closure). CBL-P was also effective in reducing migration in HCT116 and SW620 cells, with a range of closure area from 10-50%. In addition, CBL-P had antioxidant activity with IC₅₀ values of 8.549 ± 0.241 mg/mL and 2.673 ± 0.437 mg/mL for DPPH and ABTS assays, respectively. CBL-P also showed anti-inflammatory activity with the best inhibitory activity on NO production at a concentration of 40 μg/mL.

CONCLUSION

In conclusion, the mixture extract possessed antioxidant and anti-inflammatory activity. Furthermore, the mixture plant extract significantly exhibited antiproliferative and antimigration activities on SW620, HCT116, A549, and NCI-H460 cells (P ≤ 0.05). Taken together, our results suggest that medicinal plants may have synergistic effects that could potentially enhance the effectiveness of cancer treatment when used as adjuvants. These findings provide a solid scientific foundation for future efforts to explore the mechanism of action.

Discriminatory Ability and Clinical Utility of the AJCC7 and AJCC8 Staging Systems for Breast Cancer in a Middle-Income Setting

(1) Background: Differences in access to biomarker testing and cancer treatment in resource-limited settings may affect the clinical utility of the AJCC8 staging system compared to the anatomical AJCC7 system. (2) Methods: A total of 4151 Malaysian women who were newly diagnosed with breast cancer from 2010 to 2020 were followed-up until December 2021. All patients were staged using the AJCC7 and AJCC8 systems. Overall survival (OS) and relative survival (RS) were determined. Concordance-index was used to compare the discriminatory ability between the two systems. (3) Results: Migration from the AJCC7 to AJCC8 staging system resulted in the downstaging of 1494 (36.0%) patients and the upstaging of 289 (7.0%) patients. Approximately 5% of patients could not be staged using the AJCC8 classification. Five-year OS varied between 97% (Stage IA) and 66% (Stage IIIC) for AJCC7, and 96% (Stage IA) and 60% (Stage IIIC) for AJCC8. Concordance-indexes for predicting OS using the AJCC7 and AJCC8 models were 0.720 (0.694-0.747) and 0.745 (0.716-0.774), and for predicting RS they were 0.692 (0.658-0.728) and 0.710 (0.674-0.748), respectively. (4) Conclusions: Given the comparable discriminatory ability between the two staging systems in predicting the stage-specific survival of women with breast cancer in the current study, the continued use of the AJCC7 staging system in resource-limited settings seems pragmatic and justifiable.

Identification of linderalactone as a natural inhibitor of SHP2 to ameliorate CCl4-induced liver fibrosis

Liver fibrosis is characterised by the activation of hepatic stellate cells (HSCs) and matrix deposition. Accumulating evidence has revealed that the oncogenic protein tyrosine phosphatase Src homology 2 domain-containing phosphatase 2 (SHP2) acts as a therapeutic target of fibrosis. Although several SHP2 inhibitors have reached early clinical trials, there are currently no FDA-approved drugs that target SHP2. In this study, we aimed to identify novel SHP2 inhibitors from an in-house natural product library to treat liver fibrosis. Out of the screened 800 compounds, a furanogermacrane sesquiterpene, linderalactone (LIN), significantly inhibited SHP2 dephosphorylation activity in vitro. Cross-validated enzymatic assays, bio-layer interferometry (BLI) assays, and site-directed mutagenesis were used to confirm that LIN directly binds to the catalytic PTP domain of SHP2. In vivo administration of LIN significantly ameliorated carbon tetrachloride (CCl₄)-induced HSC activation and liver fibrosis by inhibiting the TGFβ/Smad3 pathway. Thus, LIN or its derivatives could be considered potential therapeutic agents against SHP2-related diseases, such as liver fibrosis or NASH.

Prognostic Significance of Preoperative Lactate Dehydrogenase to Albumin Ratio in Breast Cancer: A Retrospective Study

Purpose

We explored the relationship between platelet count to lymphocyte count ratio (PLR), monocyte count to lymphocyte count ratio (MLR), lactate dehydrogenase to albumin ratio (LAR), and long-term survival in patients with breast cancer.

Patients and Methods

We retrospectively analyzed the clinical and follow-up data of 134 patients with breast cancer. The receiver operating characteristic curve (ROC curve) was used to distinguish between the low and high ratio groups. The chi-square test or Fisher's exact test was used to calculate the differences among the investigation factors. The Kaplan-Meier method was used to draw the survival curves. Log rank test was used for univariate analysis, and Cox proportional hazards regression model was used for multivariate analysis. A P value of <0.05 was considered statistically significant.

Results

The median follow-up time was 45 months. The PFS rates in the low group (LAR≤3.4066) at 18 months, 24 months, and 36 months were 100%, 100%, and 97.6%, and those in the high group (LAR > 3.4066) were 97.7%, 94.3%, and 87.3%, respectively. LAR was associated with Age (P=0.002) and BMI (body mass index) (P=0.002). Univariate analysis showed that Tumor size (P=0.027), Node positivity (P<0.001), TNM (tumor-node-metastasis) stage (P<0.001), PLR (P=0.034), MLR (P=0.038), and LAR (P=0.035) were significantly associated with PFS (progression-free survival) in breast cancer patients. Multivariate analysis showed that Node positivity (P<0.001) and LAR (P=0.035) were associated with PFS, while PLR and MLR were not independent prognostic indicators.

Conclusion

Preoperative high LAR will be an independent predictor of prognosis in patients with breast cancer.

In Silico Characterization of Withania coagulans Bioactive Compounds as Potential Inhibitors of Hydroxymethylglutaryl (HMG-CoA) Reductase of Mus musculus

Hypercholesterolemia is a mediator for the etiology of cardiovascular diseases, which are characterized as the global leading cause of mortality. We aimed to investigate the inhibitory activity of Withania coagulans compounds against 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Hmgcr) of Mus musculus using an extensive in silico approach. The 3D structure of the Hmgcr protein is not yet known, so we performed the homology modeling using MODELLER and SWISS-MODEL tools, followed with structural validation and assessment. The PROCHECK web server showed that the top-ranked homology model from SWISS-MODEL has 93.4% of residues in the most-favorable region, the quality factor was 98%, and the Verify3D score was 91.43%, compared to the other generated models. The druggable protein-binding cavities in a 3D model of Hmgcr were investigated with the aid of commonly prescribed statin compounds using the CB-dock approach. We compiled a 3D compound library of W. coagulans, followed by drug-likeness evaluation, and found 20 eligible compounds. The pattern of consensus residues obtained from the CB-dock procedure was then used for grid-box docking of W. coagulans compounds and statin drugs using AutoDock 4.2, respectively. The results showed that withanolide R (-10.77 kcal/mol), withanolide Q (-10.56 kcal/mol), withanolide J (-10.52 kcal/mol), atorvastatin (-8.99 kcal/mol), simvastatin (-8.66 kcal/mol), and rosuvastatin (-8.58 kcal/mol) were promising candidates that bind Hmgcr protein. The key residues involved in protein-ligand (withanolide R) interactions were Y516, C526, V529, I530, M533, I535, and V537, and the formation of a H-bond was at C526, M533, and I535 residues. M533 was the consensus residue having a tendency to form a H-bond with withanolide Q, too. Molecular dynamics simulations were used to validate the top-ranked docked complexes for the stability of the modeled protein. We also predicted the pharmacokinetic properties of binding affinity-based top-ranked compounds and concluded that they could be used as potential inhibitors of Hmgcr. However, further in vitro and in vivo studies are essential to completing the drug development process.

Targeting ferroptosis: Paving new roads for drug design and discovery

Ferroptosis, first proposed in 2012, is an iron-dependent form of regulated cell death characterized by excessive polyunsaturated fatty acid oxidation. In the past decade, researchers have revealed the formation and mechanisms of ferroptosis. Cancer drug resistance can be reversed by ferroptosis induction, and inhibiting ferroptosis has been shown to block certain disease processes. As a result, several ferroptosis-targeting drugs have been developed. However, the first-generation ferroptosis-targeting agents remain hampered from clinical use, mainly due to poor selectivity and pharmacokinetics. The discoveries of FSP1, GCH1, and other potential ferroptosis-regulating pathways independent of Xc^--GSH-GPX4 provide novel targets for drug design. Recently, protein-targeted degradation and antibody-drug conjugate strategy show promise in future drug design. With novel targets, further optimizations, and new technologies, the next-generation ferroptosis-targeting agents show a promising future with improved selectivity and efficacy. In this review, we summarize mechanisms, target types, drug design, and novel technologies of ferroptosis, aiming to pave the way for future drug design and discovery in the next decade.

Metabolomic Strategies to Improve Chemical Information from OSMAC Studies of Endophytic Fungi

Metabolomics strategies are important tools to get holistic chemical information from a system, but they are scarcely applied to endophytic fungi to understand their chemical profiles of biosynthesized metabolites. Here Penicillium sp. was cultured using One Strain Many Compounds (OSMAC) conditions as a model system to demonstrate how this strategy can help in understanding metabolic profiles and determining bioactive metabolites with the application of metabolomics and statistical analyses, as well as molecular networking. Penicillium sp. was fermented in different culture media and the crude extracts from mycelial biomass (CEm) and broth (CEb) were obtained, evaluated against bacterial strains (Staphylococcus aureus and Pseudomonas aeruginosa), and the metabolomic profiles by LC-DAD-MS were obtained and chemometrics statistical analyses were applied. The CEm and CEb extracts presented different chemical profiles and antibacterial activities; the highest activities observed were against S. aureus from CEm (MIC = 16, 64, and 128 µg/mL). The antibacterial properties from the extracts were impacted for culture media from which the strain was fermented. From the Volcano plot analysis, it was possible to determine statistically the most relevant features for the antibacterial activity, which were also confirmed from biplots of PCA as strong features for the bioactive extracts. These compounds included 75 (13-oxoverruculogen isomer), 78 (austalide P acid), 87 (austalide L or W), 88 (helvamide), 92 (viridicatumtoxin A), 96 (austalide P), 101 (dihydroaustalide K), 106 (austalide k), 110 (spirohexaline), and 112 (pre-viridicatumtoxin). Thus, these features included diketopiperazines, meroterpenoids, and polyketides, such as indole alkaloids, austalides, and viridicatumtoxin A, a rare tetracycline.

Shallow- and Deep-Water Ophiura Species Produce a Panel of Chlorin Compounds with Potent Photodynamic Anticancer Activities

A Pacific brittle star Ophiura sarsii has previously been shown to produce a chlorin (3S,4S)-14-Ethyl-9-(hydroxymethyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid (ETPA) (1) with potent phototoxic activities, making it applicable to photodynamic therapy. Using extensive LC-MS metabolite profiling, molecular network analysis, and targeted isolation with de novo NMR structure elucidation, we herein identify five additional chlorin compounds from O. sarsii and its deep-sea relative O. ooplax: 10S-Hydroxypheophorbide a (2), Pheophorbide a (3), Pyropheophorbide a (4), (3S,4S,21R)-14-Ethyl-9-(hydroxymethyl)-21-(methoxycarbonyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid (5), and (3S,4S,21R)-14-Ethyl-21-hydroxy-9-(hydroxymethyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid (6). Chlorins 5 and 6 have not been previously reported in natural sources. Interestingly, low amounts of chlorins 1-4 and 6 could also be identified in a distant species, the basket star Gorgonocephalus cf. eucnemis, demonstrating that chlorins are produced by a wide spectrum of marine invertebrates of the class Ophiuroidea. Following the purification of these major Ophiura chlorin metabolites, we discovered the significant singlet oxygen quantum yield upon their photoinduction and the resulting phototoxicity against triple-negative breast cancer BT-20 cells. These studies identify an arsenal of brittle star chlorins as natural photosensitizers with potential photodynamic therapy applications.

Evidence of Insulin-Sensitizing and Mimetic Activity of the Sesquiterpene Quinone Avarone, a Protein Tyrosine Phosphatase 1B and Aldose Reductase Dual Targeting Agent from the Marine Sponge Dysidea avara

Type 2 diabetes mellitus (T2DM) is a complex disease characterized by impaired glucose homeostasis and serious long-term complications. First-line therapeutic options for T2DM treatment are monodrug therapies, often replaced by multidrug therapies to ensure that non-responding patients maintain target glycemia levels. The use of multitarget drugs instead of mono- or multidrug therapies has been emerging as a main strategy to treat multifactorial diseases, including T2DM. Therefore, modern drug discovery in its early stages aims to identify potential modulators for multiple targets; for this purpose, exploration of the chemical space of natural products represents a powerful tool. Our study demonstrates that avarone, a sesquiterpene quinone obtained from the sponge Dysidea avara, is capable of inhibiting in vitro PTP1B, the main negative regulator of the insulin receptor, while it improves insulin sensitivity, and mitochondria activity in C2C12 cells. We observe that when avarone is administered alone, it acts as an insulin-mimetic agent. In addition, we show that avarone acts as a tight binding inhibitor of aldose reductase (AKR1B1), the enzyme involved in the development of diabetic complications. Overall, avarone could be proposed as a novel natural hit to be developed as a multitarget drug for diabetes and its pathological complications.

Triple-Negative Breast Cancer and Predictive Markers of Response to Neoadjuvant Chemotherapy: A Systematic Review

Around 40-50% of all triple-negative breast cancer (TNBC) patients achieve a pathological complete response (pCR) after treatment with neoadjuvant chemotherapy (NAC). The identification of biomarkers predicting the response to NAC could be helpful for personalized treatment. This systematic review provides an overview of putative biomarkers at baseline that are predictive for a pCR following NAC. Embase, Medline and Web of Science were searched for articles published between January 2010 and August 2022. The articles had to meet the following criteria: patients with primary invasive TNBC without distant metastases and patients must have received NAC. In total, 2045 articles were screened by two reviewers resulting in the inclusion of 92 articles. Overall, the most frequently reported biomarkers associated with a pCR were a high expression of Ki-67, an expression of PD-L1 and the abundance of tumor-infiltrating lymphocytes, particularly CD8+ T cells, and corresponding immune gene signatures. In addition, our review reveals proteomic, genomic and transcriptomic markers that relate to cancer cells, the tumor microenvironment and the peripheral blood, which also affect chemo-sensitivity. We conclude that a prediction model based on a combination of tumor and immune markers is likely to better stratify TNBC patients with respect to NAC response.

Phenolic Phytochemicals for Prevention and Treatment of Colorectal Cancer: A Critical Evaluation of In Vivo Studies

Colorectal cancer (CRC) is the third most diagnosed and second leading cause of cancer-related death worldwide. Limitations with existing treatment regimens have demanded the search for better treatment options. Different phytochemicals with promising anti-CRC activities have been reported, with the molecular mechanism of actions still emerging. This review aims to summarize recent progress on the study of natural phenolic compounds in ameliorating CRC using in vivo models. This review followed the guidelines of the Preferred Reporting Items for Systematic Reporting and Meta-Analysis. Information on the relevant topic was gathered by searching the PubMed, Scopus, ScienceDirect, and Web of Science databases using keywords, such as "colorectal cancer" AND "phenolic compounds", "colorectal cancer" AND "polyphenol", "colorectal cancer" AND "phenolic acids", "colorectal cancer" AND "flavonoids", "colorectal cancer" AND "stilbene", and "colorectal cancer" AND "lignan" from the reputed peer-reviewed journals published over the last 20 years. Publications that incorporated in vivo experimental designs and produced statistically significant results were considered for this review. Many of these polyphenols demonstrate anti-CRC activities by inhibiting key cellular factors. This inhibition has been demonstrated by antiapoptotic effects, antiproliferative effects, or by upregulating factors responsible for cell cycle arrest or cell death in various in vivo CRC models. Numerous studies from independent laboratories have highlighted different plant phenolic compounds for their anti-CRC activities. While promising anti-CRC activity in many of these agents has created interest in this area, in-depth mechanistic and well-designed clinical studies are needed to support the therapeutic use of these compounds for the prevention and treatment of CRC.

Optimizing an Enzymatic Extraction Method for the Flavonoids in Moringa (Moringa oleifera Lam.) Leaves Based on Experimental Designs Methodologies

Moringa oleifera Lam. is known to have significant antioxidant properties. Because of this, the development of an optimal extraction method is crucial to obtain pharmacological products based on the bioactive compounds produced by this tree. Through a Plackett-Burman and a Box-Behnken design, enzymatic extraction conditions (temperature, agitation, solvent pH and composition, sample-to-solvent ratio, enzyme-to-sample ratio and extraction time) have been optimized using normalized areas (UA/g) as response variable and relative mass (mg/g) as quantification variable. Extractions were performed in an incubator, where all the extraction conditions could be digitally controlled. Thus, 58.9 °C, 50 rpm, 4.0 pH, 32.5% EtOH, 0.2 g sample in 15 mL solvent and 106 U/g were established as the optimal extraction conditions for the extraction with a mix of pectinases coming from Aspergillus niger. Under these optimal conditions, two-minute extractions were performed and evaluated through a single factor design. The enzymatic extraction method demonstrated its suitability to produce extracts with good antioxidant power (antioxidant activity 4.664 ± 0.059 mg trolox equivalent/g sample and total phenolic compounds 6.245 ± 0.101 mg gallic acid equivalent/g sample). The method was also confirmed to have good repeatability (1.39%) and intermediate precision (2.37%) levels.

Virucidal Activity of Lemon Essential Oil against Feline Calicivirus Used as Surrogate for Norovirus

Norovirus (NoV) is regarded as a common cause of acute gastrointestinal illness worldwide in all age groups, with substantial morbidity across health care and community settings. The lack of in vitro cell culture systems for human NoV has prompted the use of cultivatable caliciviruses (such as feline calicivirus, FCV, or murine NoV) as surrogates for in vitro evaluation of antivirals. Essential oils (EOs) may represent a valid tool to counteract viral infections, particularly as food preservatives. In the present study, the virucidal efficacy of lemon EO (LEO) against FCV was assessed in vitro. The gas chromatography hyphenated with mass spectrometry (GC/MS) technique was used to reveal the chemical composition of LEO. The following small molecules were detected as major components of LEO: limonene (53%), β-pinene (14.5%), γ-terpinene (5.9%), citral (3.8%), α-pinene (2.4%), and β-thujene (1.94%). LEO at 302.0 μg/mL, exceeding the maximum non cytotoxic limit, significantly decreased viral titre of 0.75 log₁₀ TCID50/50 μL after 8 h. Moreover, virucidal activity was tested using LEO at 3020.00 μg/mL, determining a reduction of viral titre as high as 1.25 log₁₀ TCID50/50 μL after 8 h of time contact. These results open up perspectives for the development of alternative prophylaxis approaches for the control of NoV infection.

The biological activities of quinolizidine alkaloids

Quinolizidine alkaloids isolated from various marine and terrestrial animals and plants are primarily composed of lupinine-, matrine-, and sparteine-type alkaloids. Matrine, phenanthroquinolizidines, bis-quinolizidines, and small molecules from amphibian skins are representative compounds of such alkaloids. Quinolizidine alkaloids harbor anticancer, antibacterial, antiinflammatory, antifibrosis, antiviral, and anti-arrhythmia. In this chapter, we comprehensively outline the biological activity and pharmacological action of quinolizidine alkaloids and discuss new avenues toward the discovery of novel and more efficient drugs based on these naturally occurring compounds. It is urgent for basic research and clinical practice to conduct more targeted comprehensive research based on the lead drugs of quinolizidine alkaloids with significant pharmacological activity.

Natural Agents as Novel Potential Source of Proteasome Inhibitors with Anti-Tumor Activity: Focus on Multiple Myeloma

Multiple myeloma (MM) is an aggressive and incurable disease for most patients, characterized by periods of treatment, remission and relapse. The introduction of new classes of drugs, such as proteasome inhibitors (PIs), has improved survival outcomes in these patient populations. The proteasome is the core of the ubiquitin-proteasome system (UPS), a complex and conserved pathway involved in the control of multiple cellular processes, including cell cycle control, transcription, DNA damage repair, protein quality control and antigen presentation. To date, PIs represent the gold standard for the treatment of MM. Bortezomib was the first PI approved by the FDA, followed by next generation of PIs, namely carfilzomib and ixazomib. Natural agents play an important role in anti-tumor drug discovery, and many of them have recently been reported to inhibit the proteasome, thus representing a new potential source of anti-MM drugs. Based on the pivotal biological role of the proteasome and on PIs' significance in the management of MM, in this review we aim to briefly summarize recent evidence on natural compounds capable of inhibiting the proteasome, thus triggering anti-MM activity.

Targets Involved in the Anti-Cancer Activity of Quercetin in Breast, Colorectal and Liver Neoplasms

Phytochemicals have long been effective partners in the fight against several diseases, including cancer. Among these, flavonoids are valuable allies for both cancer prevention and therapy since they are known to influence a large panel of tumor-related processes. Particularly, it was revealed that quercetin, one of the most common flavonoids, controls apoptosis and inhibits migration and proliferation, events essential for the development of cancer. In this review, we collected the evidence on the anti-cancer activity of quercetin exploring the network of interactions between this flavonol and the proteins responsible for cancer onset and progression focusing on breast, colorectal and liver cancers, owing to their high worldwide incidence. Moreover, quercetin proved to be also a potentiating agent able to push further the anti-cancer activity of common employed anti-neoplastic agents, thus allowing to lower their dosages and, above all, to sensitize again resistant cancer cells. Finally, novel approaches to delivery systems can enhance quercetin's pharmacokinetics, thus boosting its great potentiality even further. Overall, quercetin has a lot of promise, given its multi-target potentiality; thus, more research is strongly encouraged to properly define its pharmaco-toxicological profile and evaluate its potential for usage in adjuvant and chemoprevention therapy.

Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria

Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.

Bioactive compounds: a goldmine for defining new strategies against pathogenic bacterial biofilms?

Most human infectious diseases are caused by microorganisms growing as biofilms. These three-dimensional self-organized communities are embedded in a dense matrix allowing microorganisms to persistently inhabit abiotic and biotic surfaces due to increased resistance to both antibiotics and effectors of the immune system. Consequently, there is an urgent need for novel strategies to control biofilm-associated infections. Natural products offer a vast array of chemical structures and possess a wide variety of biological properties; therefore, they have been and continue to be exploited in the search for potential biofilm inhibitors with a specific or multi-locus mechanism of action. This review provides an updated discussion of the major bioactive compounds isolated from several natural sources - such as plants, lichens, algae, microorganisms, animals, and humans - with the potential to inhibit biofilm formation and/or to disperse established biofilms by bacterial pathogens. Despite the very large number of bioactive products, their exact mechanism of action often remains to be clarified and, in some cases, the identity of the active molecule is still unknown. This knowledge gap should be filled thus allowing development of these products not only as novel drugs to combat bacterial biofilms, but also as antibiotic adjuvants to restore the therapeutic efficacy of current antibiotics.

Rhodojaponin VI indirectly targets Cav2.2 channels via N-ethylmaleimide-sensitive fusion protein to alleviate neuropathic pain

Neuropathic pain is a chronic disease that severely afflicts the life and emotional status of patients, but currently available treatments are often ineffective. Novel therapeutic targets for the alleviation of neuropathic pain are urgently needed. Rhodojaponin VI, a grayanotoxin from Rhododendron molle, showed remarkable antinociceptive efficacy in models of neuropathic pain, but its biotargets and mechanisms are unknown. Given the reversible action of rhodojaponin VI and the narrow range over which its structure can be modified, we perforwmed thermal proteome profiling of the rat dorsal root ganglion to determine the protein target of rhodojaponin VI. N-Ethylmaleimide-sensitive fusion (NSF) was confirmed as the key target of rhodojaponin VI through biological and biophysical experiments. Functional validation showed for the first time that NSF facilitated trafficking of the Cav2.2 channel to induce an increase in Ca²⁺ current intensity, whereas rhodojaponin VI reversed the effects of NSF. In conclusion, rhodojaponin VI represents a unique class of analgesic natural products targeting Cav2.2 channels via NSF.

Drug delivery as a sustainable avenue to future therapies

Climate change and the need for sustainable, technological developments are the greatest challenges facing humanity in the coming decades. To address these issues, in 2015 the United Nations have established 17 Sustainable Development Goals. Anthropogenic climate change will not only affect everyone personally in the coming years, it will also reinforce the need to become more sustainable within drug delivery research. In 2021, I was appointed professor for pharmaceutical biology at the Friedrich-Alexander-University Erlangen-Nürnberg. Our research is at the interface between developing biogenic therapies and understanding of bacterial infections. In this contribution to the Orations - New Horizons of the Journal of Controlled Release, I would like to underline the need for future sustainable approaches in our research area, by highlighting selected examples from the fields of infection research, natural product characterisation and extracellular vesicles. My aim is to put into perspective current issues for these research topics, but also encourage our current student-training framework to contribute to education for sustainable development. This contribution is a personal statement to increase the overall awareness for sustainability challenges in drug delivery and beyond.

Costunolide covalently targets NACHT domain of NLRP3 to inhibit inflammasome activation and alleviate NLRP3-driven inflammatory diseases

The NLRP3 inflammasome's core and most specific protein, NLRP3, has a variety of functions in inflammation-driven diseases. Costunolide (COS) is the major active ingredient of the traditional Chinese medicinal herb Saussurea lappa and has anti-inflammatory activity, but the principal mechanism and molecular target of COS remain unclear. Here, we show that COS covalently binds to cysteine 598 in NACHT domain of NLRP3, altering the ATPase activity and assembly of NLRP3 inflammasome. We declare COS's great anti-inflammasome efficacy in macrophages and disease models of gouty arthritis and ulcerative colitis via inhibiting NLRP3 inflammasome activation. We also reveal that the α-methylene-γ-butyrolactone motif in sesquiterpene lactone is the certain active group in inhibiting NLRP3 activation. Taken together, NLRP3 is identified as a direct target of COS for its anti-inflammasome activity. COS, especially the α-methylene-γ-butyrolactone motif in COS structure, might be used to design and produce novel NLRP3 inhibitors as a lead compound.

Strategizing the human microbiome for small molecules: Approaches and perspectives

Studies of the human microbiome are providing a deeper understanding of its significance to human health, and increasing evidence links the microbiota with several diseases. Nevertheless, the exact mechanisms involved in human-microbe interactions are mostly undefined. The genomic potential of the human microbiome to biosynthesize distinct molecules outmatches its known chemical space, and small-molecule discovery in this context remains in its infancy. The profiling of microbiome-derived small molecules and their contextualization through cause-effect mechanistic studies may provide a better understanding of host-microbe interactions, guide new therapeutic interventions, and modulate microbiome-based therapies. This review describes the advances, approaches, and allied challenges in mining new microbial scaffolds from the human microbiome using genomic, microbe cultivation, and chemical analytic platforms. In the future, the complete biological characterization of a single microbe-derived molecule that has a specific therapeutic application could resolve the current limitations of microbiota-modulating therapies.

Trends in oral small-molecule drug discovery and product development based on product launches before and after the Rule of Five

In 1997, the 'Rule of Five' (Ro5) suggested physicochemical limitations for orally administered drugs, based on the analysis of chemical libraries from the early 1990s. In this review, we report on the trends in oral drug product development by analyzing products launched between 1994 and 1997 and between 2013 and 2019. Our analysis confirmed that most new oral drugs are within the Ro5 descriptors; however, the number of new drug products of drugs with molecular weight (MW) and calculated partition coefficient (clogP) beyond the Ro5 has slightly increased. Analysis revealed that there is no single scientific or technological reason for this trend, but that it likely results from incremental advances are being made in molecular biology, target diversity, drug design, medicinal chemistry, predictive modeling, drug metabolism and pharmacokinetics, and drug delivery.

Metabolomics- and systems-biology-guided discovery of metabolite lead compounds and druggable targets

Metabolomics enables the comprehensive and unbiased analysis of metabolites and lipids in biological systems. In conjunction with high-throughput activity screening, big data and synthetic biology, metabolomics can guide the discovery of lead compounds with pharmacological activity from natural sources and the gut microbiome. In combination with other omics, metabolomics can further unlock the elucidation of compound toxicity, the mode of action and novel druggable targets of disease. Here, we discuss the workflows, limitations and future opportunities to leverage metabolomics and big data in conjunction with systems and synthetic biology for streamlining the discovery and development of molecules of pharmaceutical interest.

Persicamidines-Unprecedented Sesquarterpenoids with Potent Antiviral Bioactivity against Coronaviruses

A new family of highly unusual sesquarterpenoids (persicamidines A-E) exhibiting significant antiviral activity was isolated from a newly discovered actinobacterial strain, Kibdelosporangium persicum sp. nov., collected from a hot desert in Iran. Extensive NMR analysis unraveled a hexacyclic terpenoid molecule with a modified sugar moiety on one side and a highly unusual isourea moiety fused to the terpenoid structure. The structures of the five analogues differed only in the aminoalkyl side chain attached to the isourea moiety. Persicamidines A-E showed potent activity against hCoV-229E and SARS-CoV-2 viruses in the nanomolar range together with very good selectivity indices, making persicamidines promising as starting points for drug development.

Non-hereditary early onset gastric cancer: An unmet medical need

Gastric cancer (GC) is a lethal disease and the diagnosis in the young population is a major challenge from both individual and social point of views. Early-onset GC accounts for ∼5% of GC; among them, 3% are part of a hereditary syndrome and the majority are sporadic. However, even if the early-onset forms were less frequent in the past, the increasing number in the last decades has improved the interest and awareness of them in the society and in the scientific community. In particular, the different behaviour and characteristics of early-onset GC suggest that it is a completely different entity, which requires a tailored and personalized management. Here we provide an updated overview about non-hereditary early-onset GC, which is an unmet clinical need today, along with future perspectives in this field.

The Journey of Resveratrol from Vineyards to Clinics

With rising technological advancements, several factors influence the lifestyle of people and stimulate chronic inflammation that severely affects the human body. Chronic inflammation leads to a broad range of physical and pathophysiological distress. For many years, non-steroidal drugs and corticosteroids were most frequently used in treating inflammation and related ailments. However, long-term usage of these drugs aggravates the conditions of chronic diseases and is presented with morbid side effects, especially in old age. Hence, the quest for safe and less toxic anti-inflammatory compounds of high therapeutic potential with least adverse side effects has shifted researchers' attention to ancient medicinal system. Resveratrol (RSV) - 3,4,5^' trihydroxystilbene is one such naturally available polyphenolic stilbene derivative obtained from various plant sources. For over 2000 years, these plants have been used in Asian medicinal system for curing inflammation-associated disorders. There is a wealth of in vitro, in vivo and clinical evidence that shows RSV could induce anti-aging health benefits including, anti-cancer, anti-inflammatory, anti-oxidant, phytoesterogenic, and cardio protective properties. However, the issue of rapid elimination of RSV through the metabolic system and its low bio-availability is of paramount importance which is being studied extensively. Therefore, in this article, we scientifically reviewed the molecular targets, biological activities, beneficial and contradicting effects of RSV as evinced by clinical studies for the prevention and treatment of inflammation-mediated chronic disorders.

Divergent reactivity of usnic acid and evaluation of its derivatives for antiproliferative activity against cancer cells

Natural products continue to be an inspiration for new drugs to treat debilitating diseases such as cancer. Usnic acid is a secondary metabolite isolated predominately from lichen species and has been shown to exhibit antiproliferative properties, however its application is limited by poor drug-like properties and low specificity. We report our work on investigating the reactivity of usnic acid for incorporating heterocyclic rings and the divergent reactivity that can be obtained by simply altering the reaction solvent and temperature. The synthesised derivatives were then tested against HeLa cancer cells for their antiproliferative properties. A number of promising compounds were obtained including 4, 5 and 9 that showed an IC₅₀ of 878, 311 and 116 nM, respectively, against HeLa cancer cells after 48 h of treatment.

Evaluating natural medicinal resources and their exposure to global change

Medicinal plants and their bioactive molecules are integral components of nature and have supported the health of human societies for millennia. However, the prevailing view of medicinal biodiversity solely as an ecosystem-decoupled natural resource of commercial value prevents people from fully benefiting from the capacity of nature to provide medicines and from assessing the vulnerability of this capacity to the global environmental crisis. Emerging scientific and technological developments and traditional knowledge allow for appreciating medicinal plant resources from a planetary health perspective. In this Personal View, we highlight and integrate current knowledge that includes medicinal, biodiversity, and environmental change research in a transdisciplinary framework to evaluate natural medicinal resources and their vulnerability in the anthropocene. With Europe as an application case, we propose proxy spatial indicators for establishing the capacity, potential societal benefits, and economic values of native medicinal plant resources and the exposure of these resources to global environmental change. The proposed framework and indicators aim to be a basis for transdisciplinary research on medicinal biodiversity and could guide decisions in addressing crucial multiple Sustainable Development Goals, from accessible global health care to natural habitat protection and restoration.

Impact of adjuvant chemotherapy and radiotherapy on tumour-infiltrating lymphocytes and PD-L1 expression in metastatic breast cancer

BACKGROUND

Chemotherapy and radiotherapy were postulated to induce an inflamed tumour microenvironment. We aimed to evaluate the effects of adjuvant chemotherapy/radiotherapy on tumour-infiltrating lymphocytes (TILs) and programmed death-ligand 1 (PD-L1) expression in metastatic breast cancer.

METHODS

We identified paired primary and metastatic tumours in 85 patients with breast cancer. Stromal TILs were assessed according to international guidelines. PD-L1 expression was evaluated using the VENTANA SP142 assay.

RESULTS

TILs were significantly lower in metastatic tumours than in primary tumours (12.2 vs. 8.3%, p = 0.049). PD-L1 positivity was similar between primary and metastatic tumours (21.2 vs. 14.1%, p = 0.23). TILs were significantly lower in patients who received adjuvant chemotherapy than in those who did not (-9.07 vs. 1.19%, p = 0.01). However, radiotherapy had no significant effect on TILs (p = 0.44). Decreased TILs predicted worse post-recurrence survival (hazard ratio, 2.94; 95% confidence interval [CI]: 1.41-6.13, p = 0.003), while increased TILs was associated with a better prognosis (HR, 0.12; 95% CI: 0.02-0.08, p = 0.04).

CONCLUSIONS

TILs decreased in metastatic tumours, particularly in patients who relapsed after adjuvant chemotherapy. Changes in TILs from primary to metastatic sites could be a prognostic factor after recurrence.

Machine intelligence-guided selection of optimized inhibitor for human immunodeficiency virus (HIV) from natural products

The human immunodeficiency virus (HIV) connects to the cluster of differentiation (CD4) and any of the entry co-receptors (CCR5 and CXCR4); followed by unloading the viral genome, reverse transcriptase, and integrase enzymes within the host cell. The co-receptors facilitate the entry of virus and vital enzymes, leading to replication and pre-maturation of viral particles within the host. The protease enzyme transforms the immature viral vesicles into the mature virion. The pivotal role of co-receptors and enzymes in homeostasis and growth makes the crucial target for anti-HIV drug discovery, and the availability of X-ray crystal structures is an asset. Here, we used the machine intelligence-driven framework (A-HIOT) to identify and optimize target-based potential hit molecules for five significant protein targets from the ZINC15 database (natural products dataset). Following validation with dynamic motion behavior analysis and molecular dynamics simulation, the optimized hits were evaluated using in silico ADMET filtration. Furthermore, three molecules were screened, optimized, and validated: ZINC00005328058 for CCR5 and protease, ZINC000254014855 for CXCR4 and integrase, and ZINC000000538471 for reverse transcriptase. In clinical trials, the ZINC000254014855 and ZINC000254014855 were passed in primary screens for vif-HIV-1, and we reported the specific receptor as well as interactions. As a result, the validated molecules may be investigated further in experimental studies targeting specific receptors in order to design and synergize an anti-HIV regimen.

Combinational Effect of Selected Medicinal Plants and Antibiotics Against Pathogenic Bacteria

&lt;b&gt;Background and Objective:&lt;/b&gt; The emergence of antibiotic resistance is a primary global health concern. As a result, there is an urgent need for new strategies to combat antibiotic-resistant bacteria. One of these essential strategies is the combination of medicinal plants and antibiotics as an alternative to using antibiotics alone which was the objective of this article. &lt;b&gt;Materials and Methods:&lt;/b&gt; Nine plant materials were collected from different Egypt localities and then extracted by water. Water extracts were filtered and added with Mueller-Hinton agar during preparation. Nine test bacteria and 13 standard antibiotics were used in the disc diffusion sensitivity method. &lt;b&gt;Results:&lt;/b&gt; The activity of Amikacin was increased when combined with most different plant extracts against &lt;i&gt;Escherichia coli&lt;/i&gt; while antagonistic against &lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt;. Aztreonam, Ceftriaxone, Gentamicin and Nalidixic acid antibiotics showed antagonistic or indifferent effects when combined with most different plant extracts against &lt;i&gt;E. coli&lt;/i&gt;, &lt;i&gt;Klebsiella pneumonia&lt;/i&gt; and &lt;i&gt;P. aeruginosa&lt;/i&gt;. The synergistic effect was achieved in Aztreonam when combined with all plant extracts, while Nalidixic acid showed antagonistic when combined with most plant extracts against &lt;i&gt;Proteus mirabilis&lt;/i&gt;. The antagonistic effect was achieved in Aztreonam, Ceftriaxone and Nalidixic acid when combined with &lt;i&gt;Achillea fragrantissima&lt;/i&gt;, &lt;i&gt;Artemisia monosperma&lt;/i&gt; and &lt;i&gt;Leptadenia pyrotechnica&lt;/i&gt;, also Aztreonam with &lt;i&gt;Lycium shawii&lt;/i&gt; extract against &lt;i&gt;Salmonella typhimurium&lt;/i&gt;. The &lt;i&gt;A. fragrantissima&lt;/i&gt; and &lt;i&gt;A. monosperma&lt;/i&gt; increase the activity of Novobiocin and Vancomycin against &lt;i&gt;Bacillus cereus&lt;/i&gt; and Ampicillin and Cefazolin against &lt;i&gt;Staphylococcus aureus&lt;/i&gt; but Novobiocin activity increased with most plant extracts against &lt;i&gt;S. aureus&lt;/i&gt;. &lt;b&gt;Conclusion:&lt;/b&gt; The combinations of antibiotics with the extracts of medicinal plants displayed varying degrees of effects, synergistic, antagonistic and indifferent according to antibiotic type, plant extract and test organism.

Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block

Investigating the ecological context of microbial predator-prey interactions enables the identification of microorganisms, which produce multiple secondary metabolites to evade predation or to kill the predator. In addition, genome mining combined with molecular biology methods can be used to identify further biosynthetic gene clusters that yield new antimicrobials to fight the antimicrobial crisis. In contrast, classical screening-based approaches have limitations since they do not aim to unlock the entire biosynthetic potential of a given organism. Here, we describe the genomics-based identification of keanumycins A-C. These nonribosomal peptides enable bacteria of the genus Pseudomonas to evade amoebal predation. While being amoebicidal at a nanomolar level, these compounds also exhibit a strong antimycotic activity in particular against the devastating plant pathogen Botrytis cinerea and they drastically inhibit the infection of Hydrangea macrophylla leaves using only supernatants of Pseudomonas cultures. The structures of the keanumycins were fully elucidated through a combination of nuclear magnetic resonance, tandem mass spectrometry, and degradation experiments revealing an unprecedented terminal imine motif in keanumycin C extending the family of nonribosomal amino acids by a highly reactive building block. In addition, chemical synthesis unveiled the absolute configuration of the unusual dihydroxylated fatty acid of keanumycin A, which has not yet been reported for this lipodepsipeptide class. Finally, a detailed genome-wide microarray analysis of Candida albicans exposed to keanumycin A shed light on the mode-of-action of this potential natural product lead, which will aid the development of new pharmaceutical and agrochemical antifungals.

Landscape of costimulatory molecule signature in breast cancer and its prognostic significance

Background

Breast cancer (BRCA) is the most common malignant tumor in the world. Because of its substantial heterogeneity, its clinical treatment is faced with various problems. Only a small number of patients can benefit from the treatment of immune checkpoint inhibitor (ICI). Costimulatory molecule signature (CMS) plays an essential role in T cell activation and antitumor immune response. Previous studies found that CMS is associated with prognosis-related immune response markers, suggesting that CMS may be a potential therapeutic target. However, the research on their function in BRCA subtype is still inadequate. Our study aims to analyze CMS in BRCA and establish an effective prognostic model.

Methods

We extracted 1,222 messenger RNA (mRNA) samples of 1,110 patients registered in the BRCA cohort of The Cancer Genome Atlas (TCGA), including 1,109 tumor tissue mRNA samples and 113 standard tissue samples for model construction and verification. The prognostic significance was determined by least absolute shrinkage and selection operator (LASSO)-Cox proportional hazard regression, which showed that the overall survival (OS) of the high-risk group was shorter than that of the low group (P<0.01).

Results

Although the CMS prognostic model can predict the prognosis well, the receiver operating characteristic (ROC) prediction results were unsatisfactory. The reason for this may be the heteromorphism of BRCA, so we divided the cases into four subtypes according to the PAM50 (PAM50Call_RNAseq) in clinical information. The same method was used to construct the model in the four subtypes and verify the effect of each subtype prognostic model.

Conclusions

The results showed that the submodels constructed in this study can be used to evaluate the prognosis of each subtype.

Efficacies and side effects of medicinal plants used by patients with cancer in Morocco: A retrospective treatment-outcome study

ETHNOPHARMACOLOGICAL RELEVANCE

Medicinal plants have long been used as traditional medicines in Morocco. Patients with cancer frequently use medicinal plants, with a frequency ranging from 11% to 39%. No studies have evaluated these patients in the Beni Mellal-Khenifra region.

AIM OF STUDY

We investigated the beneficial and adverse effects of medicinal plants used by patients with cancer in this region.

METHODS

We conducted a retrospective study of the outcomes of traditional treatment with medicinal plants (retrospective treatment-outcome study: RTO) in 194 patients with cancer at the regional oncology centre of Béni Mellal.

RESULTS

Beneficial effects were reported by 39% of patients. All users of the seeds of Prunus armeniaca L. reported beneficial effects (100%), followed by Curcuma longa L. (50%). We did not observe any significant difference in efficacies between the most commonly used plants (P > 0.05). Patients with cancer who had a low socioeconomic level experienced greater benefits from herbal medicines (p < 0.05). The prevalence of adverse effects was 16%. Juniperus oxycedrus L. was perceived as the most toxic plant (13 patients), as it induced significantly greater toxicity than the other plants (P < 0.05). Patients with a cancer duration of more than 12 months reported more adverse effects (p = 0.05).

CONCLUSIONS

The frequency of beneficial effects was higher than that of adverse effects. Health professionals should be aware of these effects in the process of therapeutic education. Preclinical and clinical research are considered necessary for the in-depth evaluation of the efficacies and toxicities of certain plants that have shown toxic or therapeutic potential.

Explicit molecular dynamics simulation studies to discover novel natural compound analogues as Mycobacterium tuberculosis inhibitors

Tuberculosis (TB) in one of the dreadful diseases present globally. This is caused by Mycobacterium tuberculosis. Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS) is an essential enzyme in biotin biosynthesis and is an ideal target to design and develop novel inhibitors. In order to effectively combat this disease six natural compound (butein) analogues were subjected to molecular docking to determine their binding mode and the binding affinities. The resultant complex structures were subjected to 500 ns simulation run to estimate their binding stabilities using GROMACS. The molecular dynamics simulation studies provided essential evidence that the systems were stable during the progression of 500 ns simulation run. The root mean square deviation (RMSD) of all the systems was found to be below 0.3 nm stating that the systems are well converged. The radius of gyration (Rg) profiles indicated that the systems were highly compact without any major fluctuations. The principle component analysis (PCA) and Gibbs energy landscape studies have revealed that the comp3, comp5 and comp11 systems navigated marginally through the PC2. The intermolecular interactions have further demonstrated that all the compounds have displayed key residue interactions, firmly holding the ligands at the binding pocket. The residue Lys37 was found consistently to interact with all the ligands highlighting its potential role in inhibiting the MtDTBS. Our investigation further put forth two novel compounds (comp10 and comp11) as putative antituberculosis agents. Collectively, we propose six compounds has plausible inhibitors to curtail TB and further can act as scaffolds in designing new compounds.

Targeting regulated cell death with plant natural compounds for cancer therapy: A revisited review of apoptosis, autophagy-dependent cell death, and necroptosis

Regulated cell death (RCD) refers to programmed cell death regulated by various protein molecules, such as apoptosis, autophagy-dependent cell death, and necroptosis. Accumulating evidence has recently revealed that RCD subroutines have several links to many types of human cancer; therefore, targeting RCD with pharmacological small-molecule compounds would be a promising therapeutic strategy. Moreover, plant natural compounds, small-molecule compounds synthesized from plant sources, and their derivatives have been widely reported to regulate different RCD subroutines to improve potential cancer therapy. Thus, in this review, we focus on updating the intricate mechanisms of apoptosis, autophagy-dependent cell death, and necroptosis in cancer. Moreover, we further discuss several representative plant natural compounds and their derivatives that regulate the above-mentioned three subroutines of RCD, and their potential as candidate small-molecule drugs for the future cancer treatment.

The Chemical Space of Terpenes: Insights from Data Science and AI

Terpenes are a widespread class of natural products with significant chemical and biological diversity, and many of these molecules have already made their way into medicines. In this work, we employ a data science-based approach to identify, compile, and characterize the diversity of terpenes currently known in a systematic way, in a total of 59,833 molecules. We also employed several methods for the purpose of classifying terpene subclasses using their physicochemical descriptors. Light gradient boosting machine, k-nearest neighbours, random forests, Gaussian naïve Bayes and Multilayer perceptron were tested, with the best-performing algorithms yielding accuracy, F1 score, precision and other metrics all over 0.9, thus showing the capabilities of these approaches for the classification of terpene subclasses. These results can be important for the field of phytochemistry and pharmacognosy, as they allow the prediction of the subclass of novel terpene molecules, even when biosynthetic studies are not available.

Recent Advances in Search of Bioactive Secondary Metabolites from Fungi Triggered by Chemical Epigenetic Modifiers

Genomic analysis has demonstrated that many fungi possess essential gene clusters for the production of previously unobserved secondary metabolites; however, these genes are normally reduced or silenced under most conditions. These cryptic biosynthetic gene clusters have become treasures of new bioactive secondary metabolites. The induction of these biosynthetic gene clusters under stress or special conditions can improve the titers of known compounds or the production of novel compounds. Among the inducing strategies, chemical-epigenetic regulation is considered a powerful approach, and it uses small-molecule epigenetic modifiers, which mainly act as the inhibitors of DNA methyltransferase, histone deacetylase, and histone acetyltransferase, to promote changes in the structure of DNA, histones, and proteasomes and to further activate cryptic biosynthetic gene clusters for the production of a wide variety of bioactive secondary metabolites. These epigenetic modifiers mainly include 5-azacytidine, suberoylanilide hydroxamic acid, suberoyl bishydroxamic acid, sodium butyrate, and nicotinamide. This review gives an overview on the method of chemical epigenetic modifiers to trigger silent or low-expressed biosynthetic pathways to yield bioactive natural products through external cues of fungi, mainly based on the research progress in the period from 2007 to 2022. The production of about 540 fungal secondary metabolites was found to be induced or enhanced by chemical epigenetic modifiers. Some of them exhibited significant biological activities such as cytotoxic, antimicrobial, anti-inflammatory, and antioxidant activity.

A Streptomyces Cytochrome P450 Enzyme Catalyzes Regiospecific C2-Guaninylation for the Synthesis of Diverse Guanitrypmycin Analogs

Heterologous expression of a cdps-p450 locus from Streptomyces sp. NRRL S-1521 led to the identification of guanitrypmycin D1, a new guaninylated diketopiperazine. The cytochrome P450 GutD₁₅₂₁ catalyzed the regiospecific transfer of guanine to C-2 of the indole ring of cyclo-(l-Trp-l-Tyr) via a C-C linkage and represents a new chemical transformation within this enzyme class. Furthermore, GutD₁₅₂₁ efficiently accepts several other tryptophan-containing cyclodipeptides or derivatives for regiospecific coupling with guanine, thus generating different guanitrypmycin analogs.

Forskolin affects proliferation, migration and Paclitaxel-mediated cytotoxicity in non-small-cell lung cancer cell lines via adenylyl cyclase/cAMP axis

Non-Small-Cell Lung Cancer (NSCLC) is considered one of the most frequently diagnosed cancers and the leading cause of cancer-related deaths worldwide. Despite the undoubted therapeutic advances that have occurred in clinical practice over time, due to its high degree in both heterogeneity and resistance, NSCLC remains largely incurable. As a natural cAMP elevating agent, Forskolin has shown anti-cancer properties in different tumor types, thus supposing its possible usage in treating malignancies. In this study, we investigated the Forskolin outcome in H1299 and A549 NSCLC cell lines, either alone or in combination with Paclitaxel. We proved that Forskolin impairs cell growth and migration ability of these cells, concurrently. Albeit with a different extent between H1299 and A549, changes in cell-cycle progression and epithelial-mesenchymal markers were observed in response to Forskolin administration. Interestingly, comparable cell growth impairment was also obtained with the cAMP phosphodiesterase inhibitor IBMX, while the employment of adenylyl cyclase inhibitor SQ22536 counteracted, at least in part, the Forskolin-mediated anticancer effects. Besides as a single agent, we also demonstrated that Forskolin strongly enhances Paclitaxel-induced cytotoxicity, affecting cell death mainly via apoptosis induction. Notably, H89-mediated protein kinase A (PKA) inhibition further deteriorated the combination outcome. Altogether, our data designate Forskolin as a possible anticancer molecule in NSCLC, and recognize the adenylyl cyclase/cAMP axis as one of the pathways involved in. Although achieved at preclinical stage, our findings encourage the design of future studies aimed at further exploring the Forskolin employment in NSCLC treatment.

Synthesis of Gingerol-Metals Complex and in-vitro Cytotoxic Activity on Human Colon Cancer Cell Line

Introduction

Herbs are excellent sources of medicinal substances, and their curative abilities have been recognized to treat many ailments and are used for example as antioxidants, analgesics, anti-inflammatories, antipyretics, and many other medicinal uses. The properties of natural compounds and their health effects have been studied extensively, especially those that originate from plant sources such as ginger. The ginger plant contains many chemical compounds, such as 6-gingerol, which is characterized by containing active groups such as carbonyl and hydroxide, which can be attached to metal molecules. This is what was done in this study, where the formation of complexes with a group of metals was studied and their effect on cancer cells was investigated. These complexes will open new horizons for further study of medicinal uses.

Methods

The synthesis of gingerol-metal complexes was carried out by conjugating gingerol molecules with Ag, Au, Cd, Co, Cu, Ni, and Zn metal ions. The extracted gingerol was transferred to culture tubes and deionized water-DMSO were added followed by sonication. The tubes were incubated at 90°C for two days as well as the control sample. The samples were then filtered and the complex solutions were transferred into new tubes for further studies. Different characterization techniques such as FT-IR, UV-vis spectroscopy, FESEM, and EDX are used to confirm the formation of the complexes. The in vitro of the complexes was tested by the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay against the human colorectal cancer cell lines HCT116 and HT29 which exhibited strong cytotoxicity.

Results

The gingerol-metal complexes showed an enhancement as an anticancer agent compared to the control. The in vitro anticancer activity showed that the Ag-gingerol complex showed the most activity among the other complexes.

Discussion

Gingerol-metal complexes can inhibit cancer cells, noting that the potency of the complex depends on the type of metal used.

Identifying molecular targets of Aspiletrein-derived steroidal saponins in lung cancer using network pharmacology and molecular docking-based assessments

Lung cancer is one of the leading cancers and causes of cancer-related deaths worldwide. Due to its high prevalence and mortality rate, its clinical management remains a significant challenge. Previously, the in vitro anticancer activity of Aspiletrein A, a steroid and a saponin from Aspidistra letreae, against non-small cell lung cancer (NSCLC) cells was reported. However, the anticancer molecular mechanism of other Aspiletreins from A. letreae remains unknown. Using in silico network pharmacology approaches, the targets of Aspiletreins were predicted using the Swiss Target Prediction database. In addition, key mediators in NSCLC were obtained from the Genetic databases. The compound-target interacting networks were constructed using the STRING database and Cytoscape, uncovering potential targets, including STAT3, VEGFA, HSP90AA1, FGF2, and IL2. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that several pathways were highly relevant to cancer pathogenesis. Additionally, molecular docking and molecular dynamic analyses revealed the interaction between key identified targets and Aspiletreins, including hydrogen bonding and Van der Waals interaction. This study provides potential targets of Aspiletreins in NSCLC, and its approach of integrating network pharmacology, bioinformatics, and molecular docking is a powerful tool for investigating the mechanism of new drug targets on a specific disease.

Druggable sites identification in Streptococcus mutans VicRK system evaluated by catechols

Dental caries is a global public health problem, being the most common non-communicable disease. Streptococcus mutans, the causative agent of human cariogenic dental biofilms, produce glycosyltransferases (Gtfs) whose gene expression is modulated by the VicRK system, which makes them a promising target for dental biofilm inhibitor developments. Bioinformatics have playing a significant role in drug discovery programs mainly in novel hit identification. In this study, potential inhibitors against the S. mutans VicK system have been identified through Structure-based Virtual Screening performed between the VicK druggable sites followed byMolecular Dynamic simulations (MD) with binding affinity analysis by MM-PBSA approach. First, VicK protein was downloaded from PDB, and druggability analyses were performed by PockDrug and FTMap servers describing three interaction sites (S1, S2, and S3) that covered the most important domains for stability and activity. Next, a catechol virtual screening (n = 383) was performed on AutoDock4.2, and better-docked catechols showed strong binding affinity interaction through hydrogen bonding, hydrophobic interactions, and π-stacking with VicK auto kinase and phosphatase activity sites. Ligand efficiency indexes were also calculated (LE, LELP, LLE, and BEI) and showed optimal values. Furthermore, a 200 ns MD simulation run showed stability (RMSD and RMSF) and a high number of hydrogen bonds into peltatoside and maritimein, the two best VicK complexes. These results supported that catechols could potentially inhibit exopolysaccharides synthesis and be used in the biofilm management of new anti-cariogenic and antimicrobial agents.

Natural Monoterpenes as Potential Therapeutic Agents against Atherosclerosis

Traditional herbal medicines based on natural products play a pivotal role in preventing and managing atherosclerotic diseases, which are among the leading causes of death globally. Monoterpenes are a large class of naturally occurring compounds commonly found in many aromatic and medicinal plants. Emerging evidence has shown that monoterpenes have many biological properties, including cardioprotective effects. Remarkably, an increasing number of studies have demonstrated the therapeutic potential of natural monoterpenes to protect against the pathogenesis of atherosclerosis. These findings shed light on developing novel effective antiatherogenic drugs from these compounds. Herein, we provide an overview of natural monoterpenes' effects on atherogenesis and the underlying mechanisms. Monoterpenes have pleiotropic and multitargeted pharmacological properties by interacting with various cell types and intracellular molecular pathways involved in atherogenesis. These properties confer remarkable advantages in managing atherosclerosis, which has been recognized as a multifaceted vascular disease. We also discuss limitations in the potential clinical application of monoterpenes as therapeutic agents against atherosclerosis. We propose perspectives to give new insights into future preclinical research and clinical practice regarding natural monoterpenes.

Predictive Biomarkers for Response to Immunotherapy in Triple Negative Breast Cancer: Promises and Challenges

Triple negative breast cancer (TNBC) is a highly heterogeneous disease with a poor prognosis and a paucity of therapeutic options. In recent years, immunotherapy has emerged as a new treatment option for patients with TNBC. However, this therapeutic evolution is paralleled by a growing need for biomarkers which allow for a better selection of patients who are most likely to benefit from this immune checkpoint inhibitor (ICI)-based regimen. These biomarkers will not only facilitate a better optimization of treatment strategies, but they will also avoid unnecessary side effects in non-responders, and limit the increasing financial toxicity linked to the use of these agents. Huge efforts have been deployed to identify predictive biomarkers for the ICI, but until now, the fruits of this labor remained largely unsatisfactory. Among clinically validated biomarkers, only programmed death-ligand 1 protein (PD-L1) expression has been prospectively assessed in TNBC trials. In addition to this, microsatellite instability and a high tumor mutational burden are approved as tumor agnostic biomarkers, but only a small percentage of TNBC fits this category. Furthermore, TNBC should no longer be approached as a single biological entity, but rather as a complex disease with different molecular, clinicopathological, and tumor microenvironment subgroups. This review provides an overview of the validated and evolving predictive biomarkers for a response to ICI in TNBC.

Tumor Infiltrating Lymphocytes across Breast Cancer Subtypes: Current Issues for Biomarker Assessment

Tumor-infiltrating lymphocytes (TILs) represent a surrogate biomarker of anti-tumor, lymphocyte-mediated immunity. In early, triple-negative breast cancer, TILs have level 1B of evidence to predict clinical outcomes. TILs represent a promising biomarker to select patients who can experience a better prognosis with de-intensified cancer treatments and derive larger benefits from immune checkpoint inhibitors. However, the assessment and the validation of TILs as a biomarker require a prospective and rigorous demonstration of its clinical validity and utility, provided reproducible analytical performance. With pending data about the prospective validation of TILs' clinical validity to modulate treatments in early breast cancer, this review summarizes the most important current issues and future challenges related to the implementation of TILs assessments across all breast cancer subtypes and their potential integration into clinical practice.

Engineering the biosynthesis of fungal nonribosomal peptides

Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.