Indexing Natural Products for their Antifungal Activity by Filters-based Approach: Disclosure of Discriminative Properties

Artifical intelligence: a virtual chemist for natural product drug discovery

Nature is full of a bundle of medicinal substances and its product perceived as a prerogative structure to collaborate with protein drug targets. The natural product's (NPs) structure heterogeneity and eccentric characteristics inspired scientists to work on natural product-inspired medicine. To gear NP drug-finding artificial intelligence (AI) to confront and excavate unexplored opportunities. Natural product-inspired drug discoveries based on AI to act as an innovative tool for molecular design and lead discovery. Various models of machine learning produce quickly synthesizable mimetics of the natural products templates. The invention of novel natural products mimetics by computer-assisted technology provides a feasible strategy to get the natural product with defined bio-activities. AI's hit rate makes its high importance by improving trail patterns such as dose selection, trail life span, efficacy parameters, and biomarkers. Along these lines, AI methods can be a successful tool in a targeted way to formulate advanced medicinal applications for natural products. 'Prediction of future of natural product based drug discovery is not magic, actually its artificial intelligence'Communicated by Ramaswamy H. Sarma.

Machine Learning-Enabled Genome Mining and Bioactivity Prediction of Natural Products

Natural products (NPs) produced by microorganisms and plants are a major source of drugs, herbicides, and fungicides. Thanks to recent advances in DNA sequencing, bioinformatics, and genome mining tools, a vast amount of data on NP biosynthesis has been generated over the years, which has been increasingly exploited to develop machine learning (ML) tools for NP discovery. In this review, we discuss the latest advances in developing and applying ML tools for exploring the potential NPs that can be encoded by genomic language and predicting the types of bioactivities of NPs. We also examine the technical challenges associated with the development and application of ML tools for NP research.

Alkyl Gallates as Potential Antibiofilm Agents: A Review

Biofilms, which consist of microorganisms embedded in a polymer-rich matrix, contribute to a variety of infections and increase antimicrobial resistance. Thus, there is a constant need to develop new chemotherapeutic agents to combat biofilms. This review article focuses on the use of alkyl gallates, gallic acid and its esters (methyl, ethyl, propyl, butyl, hexyl, octyl, and dodecyl gallate), most of which are found in plants, to inhibit biofilm formation. The studies under review reveal that alkyl gallates have the capacity to prevent biofilm development and eradicate mature biofilms through mechanisms that suppress the synthesis of the extracellular polymeric matrix, inhibit quorum-sensing signaling, and alter the microbial cell membrane. The effects are stronger the greater the length of the alkyl chain. Moreover, the alkyl gallates' preventive activity against biofilm formation occurs at doses below the minimum inhibitory concentration. More importantly, combining alkyl gallates with antimicrobials or blue-light irradiation produces a synergistic effect on the inhibition of biofilm formation that can be used to treat infections and overcome microbial resistance.

In Vitro Activity of Essential Oils Distilled from Colombian Plants against Candidaauris and Other Candida Species with Different Antifungal Susceptibility Profiles

Multi-drug resistant species such as Candida auris are a global health threat. This scenario has highlighted the need to search for antifungal alternatives. Essential oils (EOs), or some of their major compounds, could be a source of new antifungal molecules. The aim of this study was to evaluate the in vitro activity of EOs and some terpenes against C. auris and other Candida spp. The eleven EOs evaluated were obtained by hydro-distillation from different Colombian plants and the terpenes were purchased. EO chemical compositions were obtained by gas chromatography/mass spectrometry (GC/MS). Antifungal activity was evaluated following the CLSI standard M27, 4th Edition. Cytotoxicity was tested on the HaCaT cell line and fungal growth kinetics were tested by time–kill assays. Candida spp. showed different susceptibility to antifungals and the activity of EOs and terpenes was strain-dependent. The Lippia origanoides (thymol + p-cymene) chemotype EO, thymol, carvacrol, and limonene were the most active, mainly against drug-resistant strains. The most active EOs and terpenes were also slightly cytotoxic on the HaCaT cells. The findings of this study suggest that some EOs and commercial terpenes can be a source for the development of new anti-Candida products and aid the identification of new antifungal targets or action mechanisms.

Natural product drug discovery in the artificial intelligence era

Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.

Forty-One Plant Extracts Screened for Dual Antidiabetic and Antioxidant Functions: Evaluating the Types of Correlation between -Amylase Inhibition and Free Radical Scavenging

Dysregulation of glucose homeostasis followed by chronic hyperglycemia is a hallmark of diabetes mellitus (DM), a disease spreading as a worldwide pandemic for which there is no satisfactory dietary treatment or cure. The development of glucose-controlling drugs that can prevent complications of DM, such as hyperglycemia and oxidative stress, which contribute to the impairment of the key physiological processes in the body, is of grave importance. In pursuit of this goal, this study screened 41 plant extracts for their antidiabetic and antioxidant activities by employing assays to test for α-amylase inhibition and free radical scavenging activity (FRSA) and by measuring glucose uptake in L6-GLUT4myc cells. While extracts of Rhus coriaria, Punica granatum, Olea europaea, Pelargonium spp., Stevia rebaudiana, and Petroselinum crispum demonstrated significant α-amylase inhibition, the extracts of Rhus coriaria and Pelargonium spp. also demonstrated increased FRSA, and the extract of Rhus coriaria stimulated glucose uptake. These natural extracts, which are believed to have fewer side effects because they are prepared from edible plants, interfere with the process in the small intestine that breaks down dietary carbohydrates into monosaccharide and disaccharide derivatives, and thereby suppress increases in diet-induced blood glucose; hence, they may have clinical value for type 2 diabetes management. The Pelargonium spp. and Rhus coriaria extracts demonstrated the highest antidiabetic and antioxidant activities. Both plants may offer valuable medical benefits, especially because they can be taken as dietary supplements by patients with diabetes and can serve as sources of new, natural-based antidiabetic drug candidates. The enhancement of cellular glucose uptake stimulated by Rhus coriaria extract could lead to the development of clinical applications that regulate blood glucose levels from within the circulatory system. Isolating bioactive substances from these plant extracts and testing them in diabetic mice will significantly advance the development of natural drugs that have both antidiabetic and free radical-scavenging properties, likely with lesser side effects.

Machine learning approaches for elucidating the biological effects of natural products

Covering: 2000 to 2020 Machine learning (ML) is an efficient tool for the prediction of bioactivity and the study of structure-activity relationships. Over the past decade, an emerging trend for combining these approaches with the study of natural products (NPs) has developed in order to manage the challenge of the discovery of bioactive NPs. In the present review, we will introduce the basic principles and protocols for using the ML approach to investigate the bioactivity of NPs, citing a series of practical examples regarding the study of anti-microbial, anti-cancer, and anti-inflammatory NPs, etc. ML algorithms manage a variety of classification and regression problems associated with bioactive NPs, from those that are linear to non-linear and from pure compounds to plant extracts. Inspired by cases reported in the literature and our own experience, a number of key points have been emphasized for reducing modeling errors, including dataset preparation and applicability domain analysis.

Lauryl Gallate Activity and Streptococcus mutans: Its Effects on Biofilm Formation, Acidogenicity and Gene Expression

Streptococcus mutans bacterium is implicated in the pathogenesis of dental caries due to the production of biofilm and organic acids from dietary sucrose. Despite the availability of various means of prophylaxis, caries still has a high worldwide prevalence. Therefore, it is important to find new pharmaceuticals to inhibit S. mutans biofilm formation and acidogenicity. The aim of the current study was to evaluate the activity of lauryl gallate (dodecyl gallate) against S. mutans acidogenicity, the expression of biofilm-associated genes, and biofilm development on solid surfaces (polystyrene, glass). The biofilm quantities produced by S. mutans bacteria were assessed using colorimetric and optical profilometry techniques. Acidogenicity was evaluated by measuring the pH of the biofilm growth medium with microelectrode. Assessment of the expression of gene coding for glucan-binding protein B (gbpB), glucosyltranferases B, -C, -D (gtfB, -C, -D), and the F-ATPase β subunit of F₁ protein (atpD) was carried out using a quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The results demonstrate the capacity of lauryl gallate to significantly inhibit S. mutans acidogenicity and biofilm development on solid surfaces, in a dose-dependent manner, compared to untreated bacteria (p < 0.05). The highest activity of lauryl gallate occurred at a concentration of 98.98 µM, at which it suppressed biofilm formation by 100% and lowered pH levels by 98%. The effect of lauryl gallate treatment on gene expression changes, as demonstrated by our RT-qPCR data, was limited to the gtfD gene only, was a significant (48%) decrease in gene expression, obtained for the biofilm-producing bacteria, while a 300% increase in fold change for the same gene occurred in the planktonic cells. It is important to note that in previous studies we showed a broader effect of related derivatives. However, a similar magnitude of difference in effects between biofilm and planktonic cells for the atpD gene was obtained after treatment with octyl gallate and reverse magnitude for the same gene after treatment with ethyl gallate. Therefore, to ascertain the possible direct or indirect effects of lauryl gallate, as well as octyl gallate and ethyl gallate, more research is needed to examine the effects on the amount of enzymes and on the enzymatic activity of the products of the affected genes that are involved in the production and maintenance of biofilm by S. mutans.

Correlation between Antibacterial Activity and Free-Radical Scavenging: In-Vitro Evaluation of Polar/Non-Polar Extracts from 25 Plants

Objectives: The current study aimed to measure the antioxidant and antibacterial activities of 25 wild Palestinian edible plants, which were subjected to extraction by polar and non-polar solvents. Correlations between free radical scavenging activity and antibacterial activity of the extracts were assessed for both polar and non-polar fractions. Materials: Twenty-five wild edible plant species that are frequently consumed by people in Palestine (mainly in a rural area) were examined. Among them, 10 plant species were among those with the highest mean cultural importance values, according to an ethnobotanical survey that was conducted in the West Bank, Palestine, a few years ago. Method: The protocol of the DPPH assay for testing free-radical scavenging was utilized for determining EC50 values, while microdilution tests were conducted to determine the 50% inhibitory concentration (IC50) of the extracts for the microorganism Staphylococcus mutans. Results and Discussion: Eight extracts (non-polar fractions) were found to possess an antibacterial IC50 of less than 20 ppm, such as Foeniculum vulgare, Salvia palaestinafruticose, Micromeria fruticose, Trigonella foenum-graecum, Cichorium pumilum jacq, Salvia hierosolymitana boiss, Ruta chalepensis, and Chrysanthemum coronarium. The polar fractions possess higher antioxidant activity, while non-polar fraction possess higher antibacterial activity. Looking at all the results together can deceive and lead to the conclusion that there is no correlation between antibacterial activity against S. mutans and free radical scavenging (R2 equals 0.0538). However, in-depth analysis revealed that non-polar plant extracts with an EC50 of free radical scavenging ≤100 ppm have a four-fold order of enrichment toward more activity against S. mutans. These findings are of high importance for screening projects. A four-fold order of enrichment could save plenty of time and many in screening projects. The antibacterial active extracts marked by low-medium free radical scavenging might act through a mechanism of action other than that of highly active, free radical scavenging extracts. Conclusion: The screening of antioxidant and antimicrobial activity performed on 25 selected wild plant extracts revealed a satisfactory free radical scavenging and antimicrobial potential that could be of value in the management of oxidative stress. Further studies are recommended to explore novel and highly active natural antibacterial products.

Suppressive Effects of Octyl Gallate on Streptococcus mutans Biofilm Formation, Acidogenicity, and Gene Expression

The accumulation of biofilm by Streptococcus mutans bacteria on hard tooth tissues leads to dental caries, which remains one of the most prevalent oral diseases. Hence, the development of new antibiofilm agents is of critical importance. The current study reports the results from testing the effectiveness of octyl gallate (C8-OG) against: (1) S. mutans biofilm formation on solid surfaces (polystyrene, glass), (2) acidogenicity, (3) and the expression of biofilm-related genes. The amount of biofilm formed by S. mutans bacteria was evaluated using the colorimetric method and optical profilometry. The pH of the biofilm growth medium was measured with microelectrode. A quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was used to assess the expression of genes encoding glucan binding protein B (gbpB), glucosyltransferases B, -C, -D (gtfB, -C, -D), and the F-ATPase β subunit of the F₁ protein (atpD). The results show that C8-OG significantly diminished biofilm formation by exposed S. mutans on solid surfaces and suppressed acidogenicity in a dose-dependent manner, compared to unexposed bacteria (p < 0.05). The C8-OG concentration of 100.24 µM inhibited S. mutans biofilm development on solid surfaces by 100% and prevented a decrease in pH levels by 99%. In addition, the RT-qPCR data demonstrate that the biofilm-producing bacteria treated with C8-OG underwent a significant reduction in gene expression in the case of the four genes under study (gbpB, gtfC, gtfD, and atpD), and there was a slight decrease in expression of the gtfB gene. However, C8-OG treatments did not produce significant expression change compared to the control for the planktonic cells, although there was a significant increase for the atpD gene. Therefore, C8-OG might be a potent antibiofilm and/or anticaries agent for oral formulations that aim to reduce the prevalence of dental caries.

Phytochemical Composition and Biological Activities of Wild Scolymus maculatus L

Background: The wild population of spotted golden thistle, Scolymus maculatus, which belongs to the Compositae family, is believed to be one of the multi-curative wild plants mentioned in Flora Palaestina. This study aims to disclose the phytochemical composition, antioxidant potential, and antimicrobial activity of wild S. maculatus collected from the farms of Kabul, a village in northwest Galilee, for the first time. Methods: The phytochemical components of crude S. maculatus extracts from methanol, ethyl acetate, and n-hexane solvents were separated and identified using gas chromatography-mass spectrometry (GC-MS) in the electron impact (EI) mode. The free radical scavenging of the plant extracts was measured by DPPH assay. The microdilution test was used to determine the minimum inhibitory concentrations (MICs) of different S. maculatus extracts and to evaluate their antimicrobial activities. Results: Thirty-two phytochemicals were found in S. maculatus extracts including stigmasterol, γ-sitosterol, lupeol, lupeol acetate, and β-amyrin. Phytochemicals, such as 2-linoleoylglycerol, γ-sitosterol, β-amyrin, lupeol, (3α)-12-oleanen-3-yl acetate, and lupenyl acetate, were found to dominate the methanol extract. Most of these compounds were also observed in ethyl acetate and n-hexane extracts, but at different levels, in addition to some other minor compounds. The various extracts were investigated for their antioxidant and antimicrobial activity. The ethanolic and the methanolic extracts were shown to exhibit the highest free radical scavenging by DPPH assay with a half-maximally effective concentration (EC₅₀) of 0.37 and 0.65 mg/mL respectively, while the other three extracts (aqueous, ethyl acetate and n-hexane) were less active and their EC₅₀ (effective concentration at which DPPH radical was scavenged by 50%) were above 1.0 mg/mL. Moreover, MICs were determined to be effective against Staphylococcus aureus, Salmonella typhimurium, and Candida albicans microorganisms. Ethyl acetate and the ethanolic extracts are active against the three types of microorganisms at a minimum inhibitory concentration (MIC) of 0.5 mg/mL, while aqueous and the n-hexane extracts are inactive against Salmonella typhimurium. Conclusions: The results show that S. maculatus extracts are a rich source of compounds that can play an important role in human health, and in a broader context, in the treatment of various diseases, such antimicrobial and antioxidant-related ailments.