Artificial intelligence in microbial natural product drug discovery: current and emerging role.

Covering: up to the end of 2022Microorganisms are exceptional sources of a wide array of unique natural products and play a significant role in drug discovery. During the golden era, several life-saving antibiotics and anticancer agents were isolated from microbes; moreover, they are still widely used. However, difficulties in the isolation methods and repeated discoveries of the same molecules have caused a setback in the past. Artificial intelligence (AI) has had a profound impact on various research fields, and its application allows the effective performance of data analyses and predictions. With the advances in omics, it is possible to obtain a wealth of information for the identification, isolation, and target prediction of secondary metabolites. In this review, we discuss drug discovery based on natural products from microorganisms with the help of AI and machine learning.

Untargeted metabolomics reveals alterations in metabolites of lipid metabolism and immune pathways in the serum of rats after long-term oral administration of Amalaki rasayana.

Amalaki rasayana, a traditional preparation, is widely used by Ayurvedic physicians for the treatment of inflammatory conditions, cardiovascular diseases, and cancer. Metabolic alterations induced by Amalaki rasayana intervention are unknown. We investigated the modulations in serum metabolomic profiles in Wistar rats following long-term oral administration of Amalaki rasayana. Global metabolic profiling was performed of the serum of rats administered with either Amalaki rasayana (AR) or ghee + honey (GH) for 18 months and control animals which were left untreated. Amalaki rasayana components were confirmed from AR extract using HR-LCMS analysis. Significant reductions in prostaglandin J2, 11-dehydrothromboxane B2, and higher levels of reduced glutathione and glycitein metabolites were observed in the serum of AR administered rats compared to the control groups. Eleven different metabolites classified as phospholipids, glycerophospholipids, glucoside derivatives, organic acids, and glycosphingolipid were exclusively observed in the AR administered rats. Pathway analysis suggests that altered metabolites in AR administered rats are those associated with different biochemical pathways of arachidonic acid metabolism, fatty acid metabolism, leukotriene metabolism, G-protein mediated events, phospholipid metabolism, and the immune system. Targeted metabolomics confirmed the presence of gallic acid, ellagic acid, and arachidonic acid components in the AR extract. The known activities of these components can be correlated with the altered metabolic profile following long-term AR administration. AR also activates IGF1R-Akt-Foxo3 signaling axis in heart tissues of rats administered with AR. Our study identifies AR components that induce alterations in lipid metabolism and immune pathways in animals which consume AR for an extended period.

Urdamycin V from Streptomyces sp induces p53 independent apoptosis in cervical cancer cells inconsiderate of HPV status and inhibited growth of gram-positive human pathogens.

In cervical cancer, loss of p53 or mutant non-functional p53 and hyperactivated mTOR/Akt pathway positively correlates to cancer progression. Urdamycin V isolated from Streptomyces OA293 is a recently isolated novel angucycline derivative that in the present study showcased induction of p53 independent apoptosis in both HPV (Human papillomavirus) positive and negative cervical cancer cell lines. Apoptosis induction was via phosphorylation modulation in the cell growth regulating proteins along mTORC2/Akt/p38/Erk pathway. The compound was also tested against human pathogens and selectively inhibited gram-positive strains, Streptococcus pyogenes and Staphylococcus aureus. The present study put forward urdamycins as a potential therapeutic that places promise for further research.

Low-energy electric shock ameliorates cell proliferation, morphallaxis, and regeneration via driving key regenerative proteins in earthworm and 3T3 cells.

Electric stimulation regulates many cellular processes like cell proliferation, differentiation, apoptosis and cellular migration. Despite its crucial role in regulating stem cells and regeneration, it remains underexplored in both in-vivo and in-vitro settings. In this study, Eudrilus eugeniae are subjected to electric stimulation (1.5 V) prior and after amputation and which augments regeneration up to double-time. Blocking epimorphosis using 2 M thymidine retracts regeneration kinetics to one-third but such inhibition was rescued by applying electric stimulation which propels an overactive morphallaxis pattern of regeneration. Excreting electric stimulation on control worms shows minimal impact, whereas it enhances the key regenerative proteins like VEGF, COX2, YAP, c-Myc, and Wnt3a on amputated worms. Upon blocking epimorphosis, all these key regenerative proteins are down-regulated but through electric stimulation, the cells are reprogrammed to express a triple fold of the mentioned regenerative proteins, that further promotes morphallaxis. In 3T3 cells, electric stimulation accelerates cell proliferation and migrations in 5 secs exposure and it exerts its function by overexpressing VEGF mediated by MEK1. Wnt3a expression was gradually upregulated in increasing exposure (5 and 25 secs) which aids in maintaining the stemness property. The molecular mechanism underlying regeneration capability can assist in designing novel therapeutic applications.

Discoidin Domain Receptor 1 Inhibitors: Advances and Future Directions for Novel Therapeutics with Aid of DNA Encoded Library Screens and Artificial Intelligence.

Discoidin domain receptor (DDR) 1, a collagen binding receptor kinase, is an intensively researched therapeutic target for cancer, fibrosis and other diseases. The majority of early known DDR1 inhibitors targeted the ATP binding pocket of this enzyme that shares structural similarities with other kinase pockets across the biological system. This structural similarity of DDR1 kinase with other protein kinases often leads to "off target "toxicity issues. Understanding of uniqueness in DDR:ATP-phosphate-binding loop (P-loop), DNA encoded library screen, structure-guided optimization studies, and machine learning drug design platforms that come under the umbrella of artificial intelligence has led to the discovery of a new array of inhibitors that are highly selective for DDR1 over DDR2 and other similar kinases. Most of the drug discovery platforms concentrated on the ATP binding region of DDR1 kinase and never looked beyond this region for novel therapeutic options. Recent findings have disclosed the kinase-independent functions of DDR1 in immune exclusion, which resides in the extracellular collagen-binding domain, thus opening avenues for the development of inhibitors that veer away from targeting ATP binding pockets. This recent understanding of the functional modalities of DDR1 opens the complexity of targeting this transmembrane protein as per its functional prominence in the respective disease and thus demands the development of specific novel therapeutics. The perspective gives a short overview of recent developments of DDR1 inhibitors with the aid of the latest technologies, future directions for therapeutic development, and possibility of combinational therapeutic treatments to completely disengage functions of DDR1.

Resistance to Intervention: Paclitaxel in Breast Cancer.

Breast cancer stands as the most prevalent cancer in women globally, and contributes to the highest percentage of mortality due to cancer-related deaths in women. Paclitaxel (PTX) is heavily relied on as a frontline chemotherapy drug in breast cancer treatment, especially in advanced metastatic cancer. Generation of resistance to PTX often derails clinical management and adversely affects patient outcomes. Understanding the molecular mechanism of PTX resistance is necessary to device methods to aid in overcoming the resistance. Recent studies exploring the mechanism of development of PTX resistance have led to unveiling of a range novel therapeutic targets. PTX resistance pathways that involve major regulatory proteins/RNAs like RNF8/Twist/ROR1, TLR, ErbB3/ErbB2, BRCA1- IRIS, MENA, LIN9, MiRNA, FoxM1 and IRAK1 have expanded the complexity of resistance mechanisms, and brought newer insights into the development of drug targets. These resistance-related targets can be dealt with synthetic/natural therapeutics in combination with PTX. The present review encompasses the recent understanding of PTX resistance mechanisms in breast cancer and possible therapeutic combinations to overcome resistance.

Ellipticine, its Derivatives: Re-evaluation of Clinical Suitability with the Aid of Drug Delivery Systems.

Targeted drug delivery systems gave newer dimensions for safer and more effective use of therapeutic drugs, thus helping in circumventing the issues of toxicity and unintended drug accumulation. These ongoing developments in delivery systems can, in turn, bring back drugs that suffered various limitations, Ellipticine (EPT) being a candidate. EPT derivatives witnessed entry into clinical settings but failed to survive in clinics citing various toxic side effects. A large body of preclinical data deliberates the potency of drug delivery systems in increasing the efficiency of EPT/derivatives while decreasing their toxic side effects. Recent developments in drug delivery systems provide a platform to explore EPT and its derivatives as good clinical candidates in treating tumors. The present review deals with delivery mechanisms of EPT/EPT derivatives as antitumor drugs, in vitro and in vivo, and evaluates the suitability of EPT-carriers in clinical settings.

Molecular Networking and Whole-Genome Analysis Aid Discovery of an Angucycline That Inactivates mTORC1/C2 and Induces Programmed Cell Death.

Rediscovery of known compounds and time consumed in identification, especially high molecular weight compounds with complex structure, have let down interest in drug discovery. In this study, whole-genome analysis of microbe and Global Natural Products Social (GNPS) molecular networking helped in initial understanding of possible compounds produced by the microbe. Genome data revealed 10 biosythethic gene clusters that encode for secondary metabolites with anticancer potential. NMR analysis of the pure compound revealed the presence of a four-ringed benz[a]anthracene, thus confirming angucycline; molecular networking further confirmed production of this class of compounds. The type II polyketide synthase gene identified in the microbial genome was matched with the urdamycin cluster by BLAST analysis. This information led to ease in identification of urdamycin E and a novel natural derivative, urdamycin V, purified from Streptomyces sp. OA293. Urdamycin E (Urd E) induced apoptosis and autophagy in cancer cell lines. Urd E exerted anticancer action through inactivation of the mTOR complex by preventing phosphorylation at Ser 2448 and Ser 2481 of mTORC1 and mTORC2, respectively. Significant reduction in phosphorylation of the major downstream regulators of both mTORC1 (p70s6k and 4e-bp1) and mTORC2 (Akt) were observed, thus further confirming complete inhibition of the mTOR pathway. Urd E presents itself as a novel mTOR inhibitor that employs a novel mechanism in mTOR pathway inhibition.

PYK10, a beta-glucosidase located in the endoplasmatic reticulum, is crucial for the beneficial interaction between Arabidopsis thaliana and the endophytic fungus Piriformospora indica.

Piriformospora indica, an endophyte of the Sebacinaceae family, promotes growth and seed production of many plant species, including Arabidopsis. Growth of a T-DNA insertion line in PYK10 is not promoted and the plants do not produce more seeds in the presence of P. indica, although their roots are more colonized by the fungus than wild-type roots. Overexpression of PYK10 mRNA did not affect root colonization and the response to the fungus. PYK10 codes for a root- and hypocotyl-specific beta-glucosidase/myrosinase, which is implicated to be involved in plant defences against herbivores and pathogens. Expression of PYK10 is activated by the basic helix-loop-helix domain containing transcription factor NAI1, and two Arabidopsis lines with mutations in the NAI1 gene show the same response to P. indica as the PYK10 insertion line. PYK10 transcript and PYK10 protein levels are severely reduced in a NAI1 mutant, indicating that PYK10 and not the transcription factor NAI1 is responsible for the response to the fungus. In wild-type roots, the message level for a leucine-rich repeat protein LRR1, but not for plant defensin 1.2 (PDF1.2), is upregulated in the presence of P. indica. In contrast, in lines with reduced PYK10 levels the PDF1.2, but not LRR1, message level is upregulated in the presence of the fungus. We propose that PYK10 restricts root colonization by P. indica, which results in the repression of defence responses and the upregulation of responses leading to a mutualistic interaction between the two symbiotic partners.

Protection of mouse brain from paracetamol-induced stress by Centella asiatica methanol extract.

ETHNOPHARMACOLOGICAL RELEVANCE: Centella asiatica (CA) is a medicinal herb traditionally used as a brain tonic in Ayurvedic medicine. Various ethnomedical leads revealed the effective use of CA in the treatment of symptoms associated to oxidative stress and inflammation. AIM OF THE STUDY: The aim of this study was to evaluate the therapeutic ability of CA methanol extract (CAM) in protecting mouse brain and astrocytes from oxidative stress and inflammation induced by Paracetamol, and thus to substantiate the allied traditional/ethnomedical claims of CA. MATERIALS AND METHODS: Chemical profiling of CAM and quantification of its major constituents were carried out by HPTLC-densitometry. Mice were administered with CAM and Paracetamol in various combinations, and oxidative stress parameters (lipid peroxidation, radical scavenging) as well as nitric oxide stress were estimated from isolated mouse brain. Cellular toxicity was investigated by apoptosis/necrosis in primary astrocytes isolated from brain tissues of mouse (which was challenged by CAM/Paracetamol) by flow cytometry and fluorescent microscopy. Expression of inflammatory cytokine mediators (monocyte chemo attractant protein 1, interleukin 1, interferon γ, tumor necrosis factor ß, interleukin 10 and mitogen activated protein kinase 14 gene) in CAM/Paracetamol administered mouse brain tissues was analyzed by real time PCR. Mouse brain tissues challenged by CAM/Paracetamol were also assessed for gross and histopathology. In addition, staining with acridine orange was carried out in C6 cell lines treated with CAM, and viewed under fluorescent microscopy. RESULTS: Paracetamol elicited reactive oxygen species generation was revealed through Ferric Reducing Antioxidant Power (FRAP) activity. CAM reversed the Paracetamol induced free radical and reactive nitrogen species production and increased the scavenging activity which was more pronounced at the higher dose (80 mg/kg b.wt). CAM negated the Paracetamol-induced damage by inhibiting expression of pro-inflammatory cytokines (MCP 1, IL 1, TNF ß), and increasing the expression of the anti-inflammatory cytokine (IL 10) profoundly. Interestingly, MAPK 14 gene expression was decreased gradually and became same as normal control with increase in the dose of CAM. Also, it was evident that CAM protected mouse primary astrocytes from Paracetamol by maintaining a normal morphology. Similarly, apoptosis of primary astrocytes (treated with Paracetamol/CAM) decreased with the increase in CAM dose (80 mg/kg b.wt.) which was evident from flow cytometric data. Severe brain damage in the form of lesions was apparent from the histology of Paracetamol alone treated mouse brain. Whereas, CAM treated together with Paracetamol upturned these lesions. Surprisingly, CAM alone proved to be cytotoxic to C6 Glioma cells. CONCLUSIONS: CAM showed antioxidant and anti-inflammatory effects (which were pronounced at higher doses) against Paracetamol-induced oxidative stress and associated inflammation in mouse brain. The underlying mechanisms may be mediated by inhibiting the pro-inflammatory cytokines TNF ß, IL 1 and MCP 1 via regulation of the antioxidant mediated INF γ and MAPK 14 gene signalling pathways. The major bioactive constituents in CAM are the triterpenoid saponins, asiaticoside and madecassoside. The present results provide pharmacological evidence that CAM acts as an antioxidant and anti-inflammatory agent. Furthermore, this study validates the use of CA as an antioxidant and anti-inflammatory agent in ethnomedicine.

Streptomyces sp metabolite(s) promotes Bax mediated intrinsic apoptosis and autophagy involving inhibition of mTOR pathway in cervical cancer cell lines.

In cervical cancer, the association between HPV infection and dysregulation of phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway (PI3K/AKT/mTOR pathway) places mTOR as an attractive therapeutic target. The failure of current treatment modalities in advanced stages of this cancer and drawbacks of already available mTOR inhibitors demand for novel drug candidates. In the present study we identified the presence of a mTOR inhibitor in an active fraction of the ethyl acetate extract of Streptomyces sp OA293. The metabolites(s) in the active fraction completely inhibited mTORC1 and thereby suppressed activation of both of its downstream targets, 4E-BP1 and P70S6k, in cervical cancer cells. In addition, it also stalled Akt activation via inhibition of mTORC2. The mechanism of mTOR inhibition detailed in our study overcomes significant drawbacks of well known mTOR inhibitors such as rapamycin and rapalogs. The active fraction induced autophagy and Bax mediated apoptosis suggesting that mTOR inhibition resulted in programmed cell death of cancer cells. The molecular weight determination of the components in active fraction confirmed the absence of any previously known natural mTOR inhibitor. This is the first report of complete mTOR complex inhibition by a product derived from microbial source.

DEPTOR promotes survival of cervical squamous cell carcinoma cells and its silencing induces apoptosis through downregulating PI3K/AKT and by up-regulating p38 MAP kinase.

DEPTOR is an endogenous inhibitor of mTOR complexes, de-regulated in cancers. The present study reveals a vital role for DEPTOR in survival of cervical squamous cell carcinoma (SCC). DEPTOR was found to be overexpressed in both cervical SCC cells and tissues and it's silencing in cervical SCC cells induced apoptosis, mainly by up-regulation of p38 MAPK and by inhibiting PI3K/AKT pathway via a feed-back inhibition from mTORC1-S6K. DEPTOR silencing resulted in reduced expression of the nitric oxide synthases iNOS and eNOS, as well as increased activation of ERK1/2 and p38 MAP kinases. Activation of AKT signaling by overexpression of constitutively active-AKT (CA-AKT) failed to overcome the apoptosis caused by DEPTOR silencing. Similarly pharmacological inhibition of ERK also failed to control apoptosis. However pharmacological inhibition of p38 MAPK rescued the cells from apoptosis, indicating the major role of p38 MAPK in cell death induced by DEPTOR silencing. DEPTOR was also found to regulate ERK1/2 in an AKT dependent manner. DEPTOR knockdown induced cell death in SiHa cells overexpressing the anti-apoptotic Bcl-2 and Bcl-xL, indicating strong survival role of DEPTOR in these cells. DEPTOR overexpression activated PI3K/AKT by relieving the negative feed-back inhibition from mTORC1-S6K. DEPTOR regulation was also observed to be independent of HPV E6/E7 oncoproteins, but it might be a molecular co-factor contributing to cervical carcinogenesis. In summary, DEPTOR is found to promote survival of cervical SCC cells and its reduction induced apoptosis via differential effects on PI3K/AKT and p38 MAPK and can be a potential target in cervical SCC.