Natural products derived from medicinal plants and microbes might act as a game-changer in breast cancer: a comprehensive review of preclinical and clinical studies.

Breast cancer (BC) is the most prevalent neoplasm among women. Genetic and environmental factors lead to BC development and on this basis, several preventive - screening and therapeutic interventions have been developed. Hormones, both in the form of endogenous hormonal signaling or hormonal contraceptives, play an important role in BC pathogenesis and progression. On top of these, breast microbiota includes both species with an immunomodulatory activity enhancing the host's response against cancer cells and species producing proinflammatory cytokines associated with BC development. Identification of novel multitargeted therapeutic agents with poly-pharmacological potential is a dire need to combat advanced and metastatic BC. A growing body of research has emphasized the potential of natural compounds derived from medicinal plants and microbial species as complementary BC treatment regimens, including dietary supplements and probiotics. In particular, extracts from plants such as Artemisia monosperma Delile, Origanum dayi Post, Urtica membranacea Poir. ex Savigny, Krameria lappacea (Dombey) Burdet & B.B. Simpson and metabolites extracted from microbes such as Deinococcus radiodurans and Streptomycetes strains as well as probiotics like Bacillus coagulans and Lactobacillus brevis MK05 have exhibited antitumor effects in the form of antiproliferative and cytotoxic activity, increase in tumors' chemosensitivity, antioxidant activity and modulation of BC - associated molecular pathways. Further, bioactive compounds like 3,3'-diindolylmethane, epigallocatechin gallate, genistein, rutin, resveratrol, lycopene, sulforaphane, silibinin, rosmarinic acid, and shikonin are of special interest for the researchers and clinicians because these natural agents have multimodal action and act via multiple ways in managing the BC and most of these agents are regularly available in our food and fruit diets. Evidence from clinical trials suggests that such products had major potential in enhancing the effectiveness of conventional antitumor agents and decreasing their side effects. We here provide a comprehensive review of the therapeutic effects and mechanistic underpinnings of medicinal plants and microbial metabolites in BC management. The future perspectives on the translation of these findings to the personalized treatment of BC are provided and discussed.

In Silico Drug Discovery for Treatment of Virus Diseases.

Viral infections have remained a serious public health burden despite significant improvements in medical and pharmaceutical research in recent years. In silico approaches for drug discovery and design are fruitful for the management of a plethora of viral diseases. Virtual screening of libraries is performed using various computational tools to search for potential antiviral compounds. For this, a rational approach is used that comprises filtration of the screened compounds using docking, ligand- or pharmacophore-based similarity searches. The selected candidates are then tested in vitro to ascertain their biological activity. This minimizes the overall cost and time incurred in conventional drug designing methods. In this book chapter, we have discussed various methods of drug discovery and design, and their applications for the development of effective antiviral compounds. A descriptive methodology for the management of some common and notorious viral diseases is also outlined.

Vaccines and Immunoinformatics for Vaccine Design.

The host immune system recognizes and responds to the selective antigens or epitopes (immunome) of the intruding pathogen over an entire organism. The immune response so generated is ample to confer the desired immunity and protection to the host. This led to the conception of immunome-derived vaccines that exploit selective genome-derived antigens or epitopes from the pathogen's immunome and not its entire genome or proteome. These are designed to elicit the required immune response and confer protection against future invasions by the same pathogen. Immunoinformatics through its epitope mapping tools allows direct selection of antigens from a pathogen's genome or proteome, which is critical for the generation of an effective vaccine. This paved way for novel vaccine design strategies based on the mapped epitopes for translational applications that includes prophylactic, therapeutic, and personalized vaccines. In this chapter, various Immunoinformatics tools for epitope mapping are presented along with their applications. The methodology for immunoinformatics-assisted vaccine design is also outlined.

A study on the effect of phthalate esters and their metabolites on idiopathic infertile males.

Phthalate plasticisers in medical, cosmetic and consumer products might pose serious health implications in humans including infertility. We sought to investigate the correlation, if any, between the phthalates and their metabolites and sperm quality parameters, and male infertility. Phthalate esters (15) and their metabolites (5) were estimated in the blood serum and urine samples from the age-matched 152 infertile and 75 fertile males using gas chromatography (GC) and high-performance liquid chromatography (HPLC). Finally, the data were analysed to correlate phthalate exposure and semen quality parameters in the infertility group. The estimated levels of DEHP, DBP, DIBP, BEHIP, BPBG, DPP, DIOP, DIHP, DMP, DINP, BIOP, DMOP and DICHP were significantly higher in the infertile males compared to the fertile males (p < .05 or p < .01). However, these were not found to be associated with the semen quality parameters (sperm count, motility and sperm morphology). Similarly, HPLC data revealed that the associations between semen parameters (sperm count, sperm motility and sperm morphology) and phthalate metabolite (MEHP and MBP) concentrations in urine samples from the infertile males were mostly unremarkable or statistically nonsignificant. Conclusively, environmental exposure to phthalates and their impacts on male infertility were statistically insignificant in our study groups.

Current trends in natural products for the treatment and management of dementia: Computational to clinical studies.

The number of preclinical and clinical studies evaluating natural products-based management of dementia has gradually increased, with an exponential rise in 2020 and 2021. Keeping this in mind, we examined current trends from 2016 to 2021 in order to assess the growth potential of natural products in the treatment of dementia. Publicly available literature was collected from various databases like PubMed and Google Scholar. Oxidative stress-related targets, NF-κB pathway, anti-tau aggregation, anti-AChE, and A-ß aggregation were found to be common targets and pathways. A retrospective analysis of 33 antidementia natural compounds identified 125 sustainable resources distributed among 65 families, 39 orders, and 7 classes. We found that families such as Berberidaceae, Zingiberaceae, and Fabaceae, as well as orders such as Lamiales, Sapindales, and Myrtales, appear to be important and should be researched further for antidementia compounds. Moreover, some natural products, such as quercetin, curcumin, icariside II, berberine, and resveratrol, have a wide range of applications. Clinical studies and patents support the importance of dietary supplements and natural products, which we will also discuss. Finally, we conclude with the broad scope, future challenges, and opportunities for field researchers.

QSCR Analysis of Cytotoxicity of 6-Fluoro-3-(4H-1,2,4-triazol-3- yl)quinolin-4(1H)-ones on Chinese Hamster Ovary Cell Line: Design of REPUBLIC1986.

BACKGROUND: 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-ones are promising antitumor agents with enormous data on their profound cytotoxic effects on the human cancer cell lines. OBJECTIVES: We sought to perform a Quantitative structure cytotoxicity relationship (QSCR) analysis of a series of previously reported fluoroquinolone analogues using computerassisted multiple regression analysis and investigate the cytotoxicity-inducing structural parameters among these congeners. METHODS: The dataset was segregated into training and test sets of 6-Fluoro-3-(4H-1,2,4- triazol-3-yl)quinolin-4(1H)-ones by using a random selection method embedded in Vlife MDS 4.6 software and subjected to QSCR analysis. Next, cross-validation of the generated QSCR models was performed along with the external test set prediction. Finally, the data was analyzed and contour plots were developed to deduce the cytotoxicity-inducing structural parameters among these congeners using Minitab® software. RESULTS: The validated QSCR model exhibited a statistically significant predictive value of 92.27 percent. Our QSCR model revealed a direct proportionality between hydrogen counts and cytotoxicity, and exclusion of sulphur and nitrogen with lesser crowding of cyclopropyl rings in future potential 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-one analogues. Based on the QSCR model predictions and contour plot analysis, the de novo REPUBLIC1986 molecule provided the best hit with predicted IC50 (µM) of 0.45 against CHO cell line and is amenable to salt formation crucial for anti-ovarian cancer activity. CONCLUSION: These findings suggest the relevancy of the developed QSCR model in designing novel, potent, and safer anti-cancer drugs with 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin- 4(1H)-ones as seed compounds.

Identification of Mycoplasma pneumoniae-associated pneumonia cases among hospitalized patients using CLART® microarray technology.

OBJECTIVES: Community-acquired pneumonia (CAP) is a global health condition that affects populations from all age groups. The laboratory identification of Mycoplasma pneumoniae as a causative agent of CAP is challenging because of its atypical and fastidious nature. Therefore, this study assessed the diagnostic potential of PneumoCLART bacteria® in identifying M. pneumoniae as a causative agent of pneumonia in hospitalized adults. METHODS: This prospective study used a cross-sectional approach to assess the diagnostic potential of PneumoCLART bacteria® for detecting M. pneumoniae in sputum samples procured from 27 patients with pneumonia who required hospitalization. RESULTS: The PneumoCLART bacteria® results illustrated that 7 of 27 patients with pneumonia were positive for M. pneumoniae (26%). However, the quality of sputum varied among the M. pneumoniae-positive and M. pneumoniae-negative samples. Fifty percent of the specimens obtained from patients positive for M. pneumoniae were saliva-contaminated and unsuitable for analysis. CONCLUSIONS: Because the leukocyte count was low and sputum specimens were saliva-contaminated, these findings require further validation to prove the utility of CLART® microarray technology for the identification of M. pneumoniae in pneumonia-positive patients. Conclusively, this prospective study included a small number of clinical samples, which likely affected its outcomes.

Diagnostic parameters of the AF Genital System® for detection of Mycoplasma hominis and Ureaplasma urealyticum.

OBJECTIVE: The prevalence of Mycoplasma hominis and Ureaplasma urealyticum (genital mycoplasma) amongst Indonesian women is poorly understood because of limited availability of diagnostic techniques. We sought to compare the diagnostic parameters of the AF Genital System® with those of culture methods and PCR as the gold standard for identification of M. hominis and U. urealyticum in vaginal swab specimens. METHODS: This was an observational diagnostic study. Eighty-eight specimens were collected from patients with abnormal vaginal discharge. Detection of M. hominis and U. urealyticum was performed using the AF Genital System®, culture methods, and PCR. RESULTS: Compared with PCR and culture methods, respectively, the AF Genital System® had sensitivities of 66.6% and 57% (M. hominis) and 55.5% and 77.8% (U. urealyticum). Compared with PCR and culture methods, respectively, the AF Genital System® had specificities of 82.9% and 86.5% (M. hominis) and 82.3% and 84.8% (U. urealyticum). CONCLUSION: The sensitivity of the AF Genital System® for detection of M. hominis and U. urealyticum from vaginal swab samples was lower than that of PCR, but specificity was reasonably good (82% to 83%).

Translational Informatics for Natural Products as Antidepressant Agents.

Depression, a neurological disorder, is a universally common and debilitating illness where social and economic issues could also become one of its etiologic factors. From a global perspective, it is the fourth leading cause of long-term disability in human beings. For centuries, natural products have proven their true potential to combat various diseases and disorders, including depression and its associated ailments. Translational informatics applies informatics models at molecular, imaging, individual, and population levels to promote the translation of basic research to clinical applications. The present review summarizes natural-antidepressant-based translational informatics studies and addresses challenges and opportunities for future research in the field.

Isolation, Docking and In Silico ADME-T Studies of Acacianol: Novel Antibacterial Isoflavone Analogue Isolated from Acacia leucophloea Bark.

BACKGROUND: The plant Acacia leucophloea (Roxb.) Willd. of the family Fabaceae is of paramount importance in Indian medicine. OBJECTIVES: We sought to evaluate the in vitro anti-microbial activity of A. leucophloea stem bark extract together with its phytochemical characterization and exploration of drug-likeness attributes. METHODS: In vitro Kirby-Bauer disc-diffusion and tube-dilution assays were exploited for determining the anti-microbial activity of the methanolic bark extracts against several bacterial test strains. Spectral characterization of the isolated phytoconstituents was performed using spectroscopy techniques viz., UV, IR, 1H NMR, and mass spectroscopy followed by the in silico studies like docking and ADME-T studies. RESULTS: The crude methanolic extracts were active against all the bacterial test strains, albeit weakly or moderately, as indicated by the zone of inhibition and minimum inhibitory concentration in the anti-microbial assays. The isolated phytoconstituent was identified to be 3-(3,4-dihydro-5-methoxy-2H-chromen-6-yl)-2,5- dimethoxy-2H-chromen-7-ol (hereby coined as acacianol), a novel isoflavone analog. Acacianol demonstrated a strong binding affinity towards the bacterial DNA gyrase over clorobiocin, especially in the case of cavity 4 with no predicted toxicities in silico, except skin sensitization and chromosome damage.

Performance of TDR-300B and VITEK®2 for the identification of Pseudomonas aeruginosa in comparison with VITEK®-MS.

OBJECTIVE: Automated systems are needed for the rapid and accurate diagnosis of Pseudomonas-associated nosocomial infections among critically ill patients admitted to the intensive care unit. We assessed the performance of TDR-300B and VITEK®2 for the identification of P. aeruginosa using VITEK®-MS as the gold standard. METHODS: This analytical study employed a cross-sectional approach. First, 44 clinical isolates of P. aeruginosa were collected and refreshed. Next, a single colony of oxidase-positive, gram-negative rods (30 samples) was inoculated into a TDR-300B NF-64 card and VITEK®2 GN cassette for each isolate. Finally, bacterial identification was performed using VITEK®-MS for comparative analysis. RESULTS: Compared with the results for VITEK®-MS, the congruence rates for TDR-300B and VITEK®2 were 80.76% (21/26) and 92.30% (24/26), respectively. Further, high sensitivity was observed for TDR-300B and VITEK®2 (95.45% and 100%, respectively). In addition, TDR-300B had a lower positive predictive value and accuracy than VITEK®2, albeit without significance. CONCLUSIONS: Conclusively, there were no significant differences regarding the diagnostic efficiency of TDR-300B and VITEK®2 for P. aeruginosa.

Role of Extracellular Vesicles in Glioma Progression: Deciphering Cellular Biological Processes to Clinical Applications.

Glioma predominantly targets glial cells in the brain and spinal cord. There are grade I, II, III, and IV gliomas with anaplastic astrocytoma and glioblastoma multiforme as the most severe forms of the disease. Current diagnostic methods are limited in their data acquisition and interpretation, markedly affecting treatment modalities, and patient outcomes. Circulating extracellular vesicles (EVs) or "magic bullets" contain bioactive signature molecules such as DNA, RNA, proteins, lipids, and metabolites. These secretory "smart probes" participate in myriad cellular activities, including glioma progression. EVs are released by all cell populations and may serve as novel diagnostic biomarkers and efficient nano-vehicles in the targeted delivery of encapsulated therapeutics. The present review describes the potential of EV-based biomarkers for glioma management.

Natural Product-Based Studies for the Management of Castration-Resistant Prostate Cancer: Computational to Clinical Studies.

Background: With prostate cancer being the fifth-greatest cause of cancer mortality in 2020, there is a dire need to expand the available treatment options. Castration-resistant prostate cancer (CRPC) progresses despite androgen depletion therapy. The mechanisms of resistance are yet to be fully discovered. However, it is hypothesized that androgens depletion enables androgen-independent cells to proliferate and recolonize the tumor. Objectives: Natural bioactive compounds from edible plants and herbal remedies might potentially address this need. This review compiles the available cheminformatics-based studies and the translational studies regarding the use of natural products to manage CRPC. Methods: PubMed and Google Scholar searches for preclinical studies were performed, while ClinicalTrials.gov and PubMed were searched for clinical updates. Studies that were not in English and not available as full text were excluded. The period of literature covered was from 1985 to the present. Results and Conclusion: Our analysis suggested that natural compounds exert beneficial effects due to their broad-spectrum molecular disease-associated targets. In vitro and in vivo studies revealed several bioactive compounds, including rutaecarpine, berberine, curcumin, other flavonoids, pentacyclic triterpenoids, and steroid-based phytochemicals. Molecular modeling tools, including machine and deep learning, have made the analysis more comprehensive. Preclinical and clinical studies on resveratrol, soy isoflavone, lycopene, quercetin, and gossypol have further validated the translational potential of the natural products in the management of prostate cancer.

Natural Products for the Management of Castration-Resistant Prostate Cancer: Special Focus on Nanoparticles Based Studies.

Prostate cancer is the most common type of cancer among men and the second most frequent cause of cancer-related mortality around the world. The progression of advanced prostate cancer to castration-resistant prostate cancer (CRPC) plays a major role in disease-associated morbidity and mortality, posing a significant therapeutic challenge. Resistance has been associated with the activation of androgen receptors via several mechanisms, including alternative dehydroepiandrosterone biosynthetic pathways, other androgen receptor activator molecules, oncogenes, and carcinogenic signaling pathways. Tumor microenvironment plays a critical role not only in the cancer progression but also in the drug resistance. Numerous natural products have shown major potential against particular or multiple resistance pathways as shown by in vitro and in vivo studies. However, their efficacy in clinical trials has been undermined by their unfavorable pharmacological properties (hydrophobic molecules, instability, low pharmacokinetic profile, poor water solubility, and high excretion rate). Nanoparticle formulations can provide a way out of the stalemate, employing targeted drug delivery, improved pharmacokinetic drug profile, and transportation of diagnostic and therapeutic agents via otherwise impermeable biological barriers. This review compiles the available evidence regarding the use of natural products for the management of CRPC with a focus on nanoparticle formulations. PubMed and Google Scholar search engines were used for preclinical studies, while ClinicalTrials.gov and PubMed were searched for clinical studies. The results of our study suggest the efficacy of natural compounds such as curcumin, resveratrol, apigenin, quercetin, fisetin, luteolin, kaempferol, genistein, berberine, ursolic acid, eugenol, gingerol, and ellagic acid against several mechanisms leading to castration resistance in preclinical studies, but fail to set the disease under control in clinical studies. Nanoparticle formulations of curcumin and quercetin seem to increase their potential in clinical settings. Using nanoparticles based on betulinic acid, capsaicin, sintokamide A, niphatenones A and B, as well as atraric acid seems promising but needs to be verified with preclinical and clinical studies.

Biochemical characterization of the GTP-sensing protein, CodY of Bacillus anthracis.

The pleiotropism of the GTP-sensing transcriptional regulator CodY is evident by the gamut of processes that it regulates in almost all low G+C Gram-positive bacteria, including general metabolism, biosynthesis of some amino acids and transport systems, nitrogen uptake, sporulation, biofilm formation, motility and virulence. The role of CodY in virulence has been established in Bacillus anthracis, the top rated bioterrorism agent. In this study, we investigated the biochemical attributes of this global regulator. Homology modeling and sequence/structure analysis revealed putative GTP-binding residues in CodY of B. anthracis. CodY exhibited an interaction with the GTP as tested by ultraviolet cross-linking experiments. It could autophosphorylate itself at a conserved Ser215 residue. This was further corroborated by the impairment of autophosphorylation activity in the CodYS215A mutant. Autophosphorylation may be speculated as an additional mechanism regulating CodY activity in the cell. The protein could also hydrolyze GTP, albeit weakly, as indicated by thin- layer chromatography and spectrophotometric quantification of its kinetic parameters. Altogether, these observations provide us an insight into the mechanism of action of this global regulator and a better understanding of its functional regulation.

A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model.

The development of drug-resistant pathogenic bacteria poses challenges to global health for their treatment and control. In this context, stress response enables bacterial populations to survive extreme perturbations in the environment but remains poorly understood. Specific modules are activated for unique stressors with few recognized global regulators. The phenomenon of cross-stress protection strongly suggests the presence of central proteins that control the diverse stress responses. In this work, Escherichia coli was used to model the bacterial stress response. A Protein-Protein Interaction Network was generated by integrating differentially expressed genes in eight stress conditions of pH, temperature, and antibiotics with relevant gene ontology terms. Topological analysis identified 24 central proteins. The well-documented role of 16 central proteins in stress indicates central control of the response, while the remaining eight proteins may have a novel role in stress response. Cluster analysis of the generated network implicated RNA binding, flagellar assembly, ABC transporters, and DNA repair as important processes during response to stress. Pathway analysis showed crosstalk of Two Component Systems with metabolic processes, oxidative phosphorylation, and ABC transporters. The results were further validated by analysis of an independent cross-stress protection dataset. This study also reports on the ways in which bacterial stress response can progress to biofilm formation. In conclusion, we suggest that drug targets or pathways disrupting bacterial stress responses can potentially be exploited to combat antibiotic tolerance and multidrug resistance in the future.

Investigation of a panel of monoclonal antibodies and polyclonal sera against anthrax toxins resulted in identification of an anti-lethal factor antibody with disease-enhancing characteristics.

Hybridomas were created using spleen of mice that were actively immunized with rLFn (recombinant N-terminal domain of lethal factor). Later on, separate group of mice were immunized with rLFn to obtain a polyclonal control for passive immunization studies of monoclonal antibodies. This led to the identification of one cohort of rLFn-immnized mice that harboured disease-enhancing polyclonal antibodies. At the same time, the monoclonal antibodies secreted by all the hybridomas were being tested. Two hybridomas secreted monoclonal antibodies (H10 and H8) that were cross-reactive with EF (edema factor) and LF (lethal factor), while the other two hybridomas secreted LF-specific antibodies (H7 and H11). Single chain variable fragment (LETscFv) was derived from H10 hybridoma. H11 was found to have disease-enhancing property. Combination of H11 with protective monoclonal antibodies (H8 and H10) reduced its disease enhancing nature. This in vitro abrogation of disease-enhancement provides the proof of concept that in polyclonal sera the disease enhancing character of a fraction of antibodies is overshadowed by the protective nature of the rest of the antibodies generated on active immunization.