Physicochemical Screening Research Articles

ProT-Diff: A Modularized and Efficient Strategy for De Novo Generation of Antimicrobial Peptide Sequences by Integrating Protein Language and Diffusion Models.

Antimicrobial peptides (AMPs) are a promising solution for treating antibiotic-resistant pathogens. However, efficient generation of diverse AMPs without prior knowledge of peptide structures or sequence alignments remains a challenge. Here, ProT-Diff is introduced, a modularized deep generative approach that combines a pretrained protein language model with a diffusion model for the de novo generation of AMPs sequences. ProT-Diff generates thousands of AMPs with diverse lengths and structures within a few hours. After silico physicochemical screening, 45 peptides are selected for experimental validation. Forty-four peptides showed antimicrobial activity against both gram-positive or gram-negative bacteria. Among broad-spectrum peptides, AMP_2 exhibited potent antimicrobial activity, low hemolysis, and minimal cytotoxicity. An in vivo assessment demonstrated its effectiveness against a drug-resistant E. coli strain in acute peritonitis. This study not only introduces a viable and user-friendly strategy for de novo generation of antimicrobial peptides, but also provides potential antimicrobial drug candidates with excellent activity. It is believed that this study will facilitate the development of other peptide-based drug candidates in the future, as well as proteins with tailored characteristics.

Quality Assessment of Gloriosa superba L. Tuber Natural Populations of Telangana, India Based on Physico-Chemical Screening and Colchicine Quantification

Quality Assessment of Gloriosa superba L. Tuber Natural Populations of Telangana, India Based on Physico-Chemical Screening and Colchicine Quantification

Machine learning models and performance dependency on 2D chemical descriptor space for retention time prediction of pharmaceuticals

The predictive modeling of liquid chromatography methods can be an invaluable asset, potentially saving countless hours of labor while also reducing solvent consumption and waste. Tasks such as physicochemical screening and preliminary method screening systems where large amounts of chromatography data are collected from fast and routine operations are particularly well suited for both leveraging large datasets and benefiting from predictive models. Therefore, the generation of predictive models for retention time is an active area of development. However, for these predictive models to gain acceptance, researchers first must have confidence in model performance and the computational cost of building them should be minimal. In this study, a simple and cost-effective workflow for the development of machine learning models to predict retention time using only Molecular Operating Environment 2D descriptors as input for support vector regression is developed. Furthermore, we investigated the relative performance of models based on molecular descriptor space by utilizing uniform manifold approximation and projection and clustering with Gaussian mixture models to identify chemically distinct clusters. Results outlined herein demonstrate that local models trained on clusters in chemical space perform equivalently when compared to models trained on all data. Through 10-fold cross-validation on a comprehensive set containing 67,950 of our company's proprietary analytes, these models achieved coefficients of determination of 0.84 and 3 % error in terms of retention time. This promising statistical significance is found to translate from cross-validation to prospective prediction on an external test set of pharmaceutically relevant analytes. The observed equivalency of global and local modeling of large datasets is retained with METLIN's SMRT dataset, thereby confirming the wider applicability of the developed machine learning workflows for global models.

A new polyene macrolide antibiotic, machidamycin, produced by Streptomyces sp. K22-0017.

A new polyene macrolide, machidamycin (1), and a known compound YS-822A (2), were obtained by physicochemical screening from a culture broth of Streptomyces sp. K22-0017. The structures were elucidated using MS and 1D/2D NMR analyses. Compound 1 exhibited weak antifungal activity against Candida albicans and Mucor racemosus. Furthermore, 1 showed stronger antileishmanial activity than the existing drug paromomycin.

Binding Mode-Based Physicochemical Screening Method Using d-Ala-d-Ala Silica Gel and Chemical Modification Approach to Facilitate Discovery of New Macrolactams, Banglactams A and B, from Nonomuraea bangladeshensis K18-0086.

Utilizing a binding mode-based physicochemical screening method using d-Ala-d-Ala silica gel, two new macrolactams, named banglactams A (1) and B (2), were discovered from the culture broth of Nonomuraea bangladeshensis K18-0086. In the course of our investigation, we found that d-Ala-d-Ala silica gel precisely differentiated the chemical structures of banglactams and separated them. However, we were not able to obtain enough of 1 to elucidate the structure due to its instability and insolubility. To overcome this challenge, we chemically modified 1 to improve solubility, enabling us to obtain a sufficient material supply for the indirect determination of the structure. Antibacterial activity evaluation of banglactams revealed that 1 binding to d-Ala-d-Ala silica gel exhibited antibacterial activity against Staphylococcus aureus; however, this was not the case with 2. This research indicates the utility of our original binding mode-based PC screening method, and the combination strategy of PC and chemical modifications led us to discover novel antibacterial compounds.

Phytochemical Evaluation of Selected Ayurvedic Formulations and Evaluate their Antioxidant Activity

Abstract: The Ayurvedic formulations' evaluation is very wide and deep. The project's goal was to evaluate the phytochemistry and antioxidant activity of Ayurvedic formulations used to treat digestive disorders. Herbal formulations are typically available as single or mixed formulations of multiple plant constituents, and it is critical to quantify the number of markers present in such formulations to ensure the product's high quality. The extract of formulations (Ajmodadi churna, Avipattikar churna, and Sanjivani vati) was subjected to physicochemical screening, phytochemical screening, HPTLC, and antioxidant activity was observed in the current study. Three ayurvedic formulations (Sanjivini vati, Ajmodadi Churna, and Avipattikar Churna) were studied physicochemically in this study. The extraction process determined the total phenolic and flavonoid content. The antioxidant capacity of the selected formulation was calculated by three methods; total antioxidant capacity, ferric- reducing power, and DPPH scavenging activity. The active constituent was isolated using the HPTLC method. This study shows that the formulations Ajmodai churna, Avipattikar churna, and Sanjivani vati are important sources of antioxidant compounds. The active constituent was isolated using the HPTLC method. The HPTLC technique showed the presence of phenolics and terpenoids that are responsible for antioxidant activity. Phenolics and Terpenoids, due to their antioxidant activity, are used as an important source for digestive disorders.

Virgaricins C and D, new pramanicin analogs produced by Apiospora sp. FKI-8058.

Two new pramanicin analogs, named virgaricins C (1) and D (2), were discovered by physicochemical screening from a static cultured material of Apiospora sp. FKI-8058. Their structures were elucidated by MS and NMR analyses and chemical derivatization. Compounds 1 and 2 showed moderate antimalarial activity and cytotoxicity.

Design and Synthesis of d-Ala-d-Ala Silica Gel for a Binding Mode-Based Physicochemical Screening Method.

Vancomycin is a potent and broad-spectrum antibiotic that binds to the d-Ala-d-Ala moiety of the growing bacterial cell wall and kills bacteria. This fascinating binding model prompted us to design and synthesize d-Ala-d-Ala silica gels for the establishment of a new physicochemical (PC) screening method. In this report, we confirmed that vancomycin binds to d-Ala-d-Ala silica gel and can be eluted with MeOH containing 50 mM TFA. Finally, d-Ala-d-Ala silica gel enables to purify vancomycin from the culture broth of a vancomycin-producing strain, Amycolatopsis orientalis.

P16-50: Physicochemical screening and preliminary in vitro assessment of Galium verum L. alcoholic extract

P16-50: Physicochemical screening and preliminary in vitro assessment of Galium verum L. alcoholic extract

Genomic analysis and physicochemical screening of ikarugamycin, fumaquinone, and a new compound, pudicin from Streptomyces sp. 3MP-14

Genomic analysis and physicochemical screening of ikarugamycin, fumaquinone, and a new compound, pudicin from Streptomyces sp. 3MP-14

Pharmacognostic evaluation and physicochemical screening of the rhizomes of Zingiber officinale (Ginger)

Pharmacognostic evaluation and physicochemical screening of the rhizomes of Zingiber officinale (Ginger)

Anti-uropathogenic, antioxidant and struvite crystallization inhibitory potential of fresh and fermented coconut water

Coconut water treats many health issues, including kidney stones and urinary tract infections. However, the therapeutic application of coconut water to treat urolithiasis has remained an unexplored topic. This study compares the effect of fresh coconut water (CW) and naturally fermented coconut water (FCW) on anti-uropathogenic, antioxidant, and anti-urolithiasis activities. Initial physicochemical screening established that CW is a rich source of total phenolics, protein, and minerals. Further, the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay showed that CW and FCW have an antioxidant potential of 48.33 ± 2.52% and 55.12 ± 2.99%, respectively. While the FCW-treated cultures of selected uropathogens showed antimicrobial activity, the CW-treated cultures displayed negligible activity. Subsequently, anti-struvite analysis was performed using the single gel diffusion method, where different concentrations of CW and FCW were treated during struvite crystallization under in vitro conditions. The increasing concentrations of CW and FCW decreased the number and size of struvite crystals that grew in the gel medium. These results indicate that CW has antioxidant property and a marginal inhibitory effect during in vitro struvite crystallization but is not anti-uropathogenic. However, FCW shows potential antioxidant, anti-uropathogenic, and anti-struvite urolithiatic properties. Further, FTIR, SEM, and XRD techniques were used to confirm the impact of CW or FCW on struvite crystallization.

Detection and characterization of new mangromicin analogs by tandem mass spectrometry.

Many useful natural products are usually screened based on their biological activities. On the other hand, various natural products can be detected based on their physicochemical properties. We have already reported the isolation and characterization of mangromicins from a cultural broth of Lechevalieria aerocolonigenes K10-0216 using physicochemical screening. In this report, we have conducted the mass spectrometry-based screening of new mangromicin analogs based on the neutral loss pattern originated from the unique cyclopentadecane skeleton of mangromicins. Two novel analogs were detected showing characteristic neutral loss pattern found in eight known mangromicin analogs. We propose the structures of the newly-found analogs based on the mass spectrometric as well as genomic and metabolic pathway data.

Physicochemical screening and antibacterial activity of fresh water macroalgae (L.) Kutz

The plant kingdom is rich in bioactive natural compounds, and extracts from various plants, as well as red, green, and brown macro and micro algae, can be used. is one of the largest filamentous green-alga genus. The majority of Cladophora species can be found all over the world, in both temperate and tropical climates. They are rich in secondary metabolites. The dried algal mass was crushed into a fine powder and acetone extract was used for phytochemical screening. Phytochemical analysis showed the presence of various secondary metabolites like alkaloids, alkaloids, steroids, flavonoids, carbohydrates, and proteins. Antibacterial activity of against showed positive results.

Nephroprotective Effect of Asparagus africanus Lam. Root Extract against Gentamicin-Induced Nephrotoxicity in Swiss Albino Mice.

The kidney is the organ most vulnerable to nephrotoxic drugs such as gentamicin. Nephrotoxicity is a rapid deterioration of kidney function due to various factors. Gentamicin causes nephrotoxicity, which was manifested by an increase in serum kidney biomarkers. Asparagus africanus is one of the ethnomedicinal plants used as traditional medicine for treating various ailments, including kidney disease in Ethiopian society. Thus, the aim of this study is to evaluate the nephroprotective effect of A. africanus root extract on gentamicin-induced nephrotoxicity. Using maceration techniques, 100 g of dried plant powder was extracted in 1 L of ethanol. The physicochemical screening of plant extracts revealed the presence of flavonoids, phenols, tannins, saponins, and steroids. The nephroprotective activity of A. africanus crude extract was evaluated on male Swiss albino mice. The crude ethanolic extract at 200 and 400 mg/kg doses showed strong nephroprotective effects by restoring biomarkers such as creatinine, uric acid, and blood urea nitrogen, which were damaged by gentamicin (p < 0.05) in a dose-dependent manner. The mice treated with higher doses (400 mg/kg) had a comparable nephroprotective effect compared to the positive control group (200 mg/kg silymarin; p > 0.05). The histopathology of the control group showed normal glomeruli, normal parenchyma, distal convoluted, and no tubular damage. The toxicant-induced group showed damage to glomeruli and inflammatory infiltration. Therefore, A. africanus root extract has a nephroprotective activity by retarding the gentamicin toxicity in male Swiss albino mice.

A Review on Pharmacognostic, Phytochemical and Biological Potential of Gmelina Arborea Roxb (Shivan Plant)

Gmelina arborea Roxb belonging to family Lamiaceae. It is a fast growing deciduous tree, having vast medicinal importance and is one of the ingredients of dashamoola used in Ayurveda. As Dashamoola has kapha vata hara property and is well known in treating vata vyadhi, Gmelina arborea being the member of dashamoola is also said to have similar properties. Any plant which is used medicinally requires detailed study prior to its use because for the purpose of identification of the plant, to avoid the admixture of other drugs and also for its therapeutic efficacy the present study was undertaken to lay down pharmacognostical and physicochemical standards for Gambhari leaf. Pharmacognostical study reveals Moisture content, Total ash value, water and Acid insoluble value. Extractive value and alcoholic and aqueous extract respectively. Microscopic and Macroscopic evaluations. Leaf constants like stomatal variety, stomatal index, vein islet number, vein termination variety even have been given. Phytochemical screening showed the presence of Alkaloids, Carbohydrate, coumarins, steroids, Tannins. Medicinal uses of its roots, leaves, flowers, fruit, bark, pharmacological activity The roots, fruits and the leaves of Gambhari have countless medicinal value therefore traditionally it was commonly used as anthelmintic, antimicrobial, anti-diabetic, anti-aging, analgesic, diuretic, hepato-protective and antiepileptic agent. There is a lots of medicinal properties present in the Gmelina arborea plant. The present article gives all necessary information on plant. Keywords: Dashamoola, Gmelina arborea, Physico-chemical screening, Pharmacological activity, Medicinal uses.

Shikinefragalides A-D, new tricyclic macrolides produced by Stachybotryaceae sp. FKI-9632.

Four new tricyclic macrolides, named shikinefragalides A (1), B (2), C (3) and D (4), were isolated by physicochemical (PC) screening from a static culture material of Stachybotryaceae sp. FKI-9632. Their structures were elucidated as new analogs of colletofragarones by MS and NMR analyses. Compounds 1 and 2 showed weak antimalarial activity and cytotoxicity.

ORGANIC AND INORGANIC PHYTOCHEMICAL SCREENING, QUANTITATIVE ANALYSIS OF ALKALOIDS OF STEM AND ROOT EXTRACT OF LAVANGA

Introduction: Lavanga is one of the most ancient and valuable spices due to its versatile uses in treatment according to Ayurveda lavanga has tikta and katu rasa and sheeta virya. Due to katu rasa it acts as kaphashamaka and pittahara due to sheeta veerya. Lavanga contains most of various secondary metabolites with great potentials. Materials &amp;Methods Aims &amp; objectives: The aim to study is to evaluate organic and inorganic screening and Quantitative analysis of alkaloids of stem and root extract of lavanga. Qualitative analysis like phytochemical screening and inorganic screening were carried out and physico chemical screening with standard techniques. Quantitative analysis like quantification of alkaloids were estimated by Harborne method. Results: Qualitative organic and inorganic screening showed the presence of carbohydrates, saponin, flavonoids, steroids, alkaloids, glycoside in aqueous extract, alkaloids, proteins and amino acids, Quinone and glycoside are present in ethanolic extract. Inorganic elemental analysis shows presence of calcium, Iron, sodium are appreciated in the stem and root of lavanga extract. Quantification of alkaloids shown 24.2 % of alkaloids presence. Conclusion: Lavanga stem&amp; root extract shows many compounds in aqueous extract than alcoholic extract and higher alkaloids presence in stem and root of lavanga &amp; justifies their uses for human health benefit

Microbial and Physicochemical Screening of Ready to Eat Street Foods

Food samples: African salad, fried yam, fried potato, fried plantain, bole and suya meat retailed in three locations along Choba, Aluu and Alakahia were analyzed for their microbial load. Analysis of the food samples revealed Total viable count ranging from 3.8×107 cfu/g to 5.2×107 cfu/g (African salad), 2.6×107 cfu/g to 3.3×107 cfu/g (Bole), 3.0×107 cfu/g to 3.4×107 cfu/g (Plantain), 3.4×107 cfu/g to 3.6×107 cfu/g (Potato), 2.9×107 cfu/g to 3.3×107 cfu/g (Yam) and 4.8×107 cfu/g to 5.1×107 cfu/g (Suya meat) from the various locations. The organism isolated includes, Staphylococcus aureus (25%), Escherichia coli (25%), Pseudomonas (15%), Streptococcus (15%), Bacillus cereus (12%) and Salmonella spp (8%). The TVC count in these food samples exceeds the standard set by International Commission for Microbiology Specification for Food (ICMSF) for ready-to-eat food which states that TVC count between 0-107 cfu/g is acceptable, 104 to 105 cfu/g is tolerable and &gt;107 cfu/g is unacceptable. Therefore, these foods are not bacteriologically fit for consumption. The occurrence of these bacterial isolates in the foods constitutes public health risk to consumers as these pathogens have been associated with foodborne infections Therefore, government should enforce strong food safety regulations for street foods vendors. In addition, street food vendors need to be educated on food safety and hygienic practices

Phytochemical characterization, and antioxidant and antibacterial activities of the hydroethanolic extract of Anadenanthera peregrina stem bark.

The Brazilian Cerrado biome consists of a great variety of endemic species with several bioactive compounds, and Anadenanthera peregrina (L.) Speg is a promising species. In this study, we aimed to perform phytochemical characterization and evaluate the antioxidant and antibacterial activities against Staphylococcus aureus and Escherichia coli of the hydroethanolic extract of A. peregrina stem bark. The barks were collected in the Botanical Garden of Goiânia, Brazil. The hydroethanolic extract was obtained by percolation and subjected to physicochemical screening, total phenolic content estimation, high-performance liquid chromatography (HPLC) fingerprinting, and antioxidant (IC50 values were calculated for the 2,2-diphenyl-1-picrylhydrazyl assay - DPPH) and antibacterial activity determination. The pH of the extract was 5.21 and density was 0.956 g/cm3. The phytochemical screening indicated the presence of cardiac glycosides, organic acids, reducing sugars, hemolytic saponins, phenols, coumarins, condensed tannins, flavonoids, catechins, depsides, and depsidones derived from benzoquinones. The extract showed intense hemolytic activity. The total phenolic content was 6.40 g GAE 100 g-1. The HPLC fingerprinting analysis revealed the presence of gallic acid, catechin, and epicatechin. We confirmed the antioxidant activity of the extract. Furthermore, the extract did not inhibit the growth of E. coli colonies at any volume tested, but there were halos around S. aureus colonies at all three volumes tested. These results contribute to a better understanding of the chemical composition of A. peregrina stem bark and further support the medicinal applications of this species.