Metabophore-mediated retro-metabolic ('MeMeReMe') approach in drug design.

Preclinical toxicity assessments of new drugs require the use of in silico prediction techniques as ethics, cost, time, and complexity limit in vitro and in vivo methods. This review discusses the fundamental concepts of biophores especially toxicophores and their detection methodologies, tools and techniques, as well as ongoing challenges, and methods for overcoming them. This will guide the design community in manipulating lead compounds via a pre-determined pathway based on the MeMeReMe approach.

Characterization of a putative metal-dependent PTP-like phosphatase from Lactobacillus helveticus 2126.

To date, there are very limited reports on sequence analysis and structure-based molecular modeling of phosphatases produced by probiotic bacteria. Therefore, a novel protein tyrosine-like phosphatase was characterized from L. helveticus 2126 in this study.

Training recurrent neural networks as generative neural networks for molecular structures: how does it impact drug discovery?

Introduction: Deep learning approaches have become popular in recent years in de novo drug design. Generative models for molecule generation and optimization have shown promising results. Molecules trained on different chemical data could regenerate molecules that were similar to the query molecule, thus supporting lead optimization.

The forgotten sugar: A review on multifarious applications of melezitose.

Although, 187 years elapsed after the discovery of melezitose, it is a high time to deduce some solid applications as there are only 13 more years left to celebrate a double century of this sugar. The forgotten sugar has multifarious applications; it is used as a metabolic marker to differentiate melezitose fermenting microorganisms, as a carbon source to culture specific microorganisms, as a potential surfactant and excipient to stabilize pharmaceuticals, as a lyoprotectant or cryoprotectant for several industrial applications, as an edibility enhancer in food industry, as a hair smoothening agent in cosmetic industry, and provide protective & nourishing effects in fisheries and aquaculture industries. In entomological research, it is used to study niche differentiation, increased longevity of insects and also as a biocontrol agent.

Health Benefits of Fermented Bamboo Shoots: The Twenty-First Century Green Gold of Northeast India.

The word "bamboo" reminds us of "a hollow stick," but it is filled with a plethora of health benefits. The tribals of northeastern India ferment these beneficial bamboo shoots for the goodness of mankind. Fermentation is an important age-old biotechnological procedure used for the preservation of food products.

Probiotic Validation of a Non-native, Thermostable, Phytase-Producing Bacterium: Streptococcus thermophilus.

Phytate-linked nutritional deficiency disorders have plagued poultry for centuries. The application of exogenous phytases in poultry feed has served as a solution to this problem. However, they are linked to certain limitations which include thermal instability during prolonged feed processing.

Machine learning models for drug-target interactions: current knowledge and future directions.

Predicting the binding affinity between compounds and proteins with reasonable accuracy is crucial in drug discovery. Computational prediction of binding affinity between compounds and targets greatly enhances the probability of finding lead compounds by reducing the number of wet-lab experiments. Machine-learning and deep-learning techniques using ligand-based and target-based approaches have been used to predict binding affinities, thereby saving time and cost in drug discovery efforts.

An in vitro chicken gut model for the assessment of phytase producing bacteria.

An in vitro simulated chicken gut model was proposed for studying the phytase activity of selected bacteria such as , , , and using known probiotic bacterium, as a control. The selected bacteria were viable in the intestinal lumen and produced extracellular phytase at optimal phytate concentration of 6.25 mM when compared to 3.

Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts.

Tetherin, an interferon-induced host protein encoded by the bone marrow stromal antigen 2 (BST2/CD317/HM1.24) gene, is involved in obstructing the release of many retroviruses and other enveloped viruses by cross-linking the budding virus particles to the cell surface. This activity is antagonized in the case of human immunodeficiency virus (HIV)-1 wherein its accessory protein Viral Protein U (Vpu) interacts with tetherin, causing its downregulation from the cell surface.

A Preliminary Study on Probiotic Characteristics of Sporosarcina spp. for Poultry Applications.

Probiotics are well known for their wide range of beneficial activities. However, recent use of probiotic Bifidobacterium, Enterococcus, and Lactobacillus spp. has been plagued by certain disadvantages such as complex growth requirements, high maintenance cost, susceptibility to the gastrointestinal environment, pathogenic gene transfer, non-standardized dosage, cell lysis at extreme acidic pH, widespread antibiotic resistance, and lower bacterial viability due to the lack of spore formation.

Microbial degradation of -inositol hexakisphosphate (IP6): specificity, kinetics, and simulation.

Microbial degradation of -inositol hexakisphosphate (IP6) is crucial to deal with nutritional problems in monogastric animals as well as to prevent environmental phosphate pollution. The present study deals with the degradation of IP6 by microorganisms such as spp. and .

Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective.

HIV-1 being the most widespread type worldwide, its accounts for almost 95% of all infections including HIV associated dementia (HAD) that triggers neurological dysfunction and neurodegeneration in patients. The common features associated with HAD and other neurodegenerative diseases are accumulation of amyloid plaques, neuronal loss and deterioration of cognitive abilities, amongst which amyloid fibrillation is considered to be a hallmark. The success of effective therapeutics lies in the understanding of mechanisms leading to neurotoxicity.

A comprehensive review of patented antileishmanial agents.

On 14 October 2010, the WHO reported that more than 1 billion people worldwide who live in remote rural areas are affected by neglected tropical diseases. Leishmaniasis is caused by protozoa of more than 20 different species in humans. The three major forms of disease are cutaneous, mucocutaneous and visceral leishmaniasis (VL).

JUZBOX: a web server for extracting biomedical words from the protein sequence.

Unlabelled: The recognition of gene/protein names in literature is one of the pivotal steps in the processing of biological literatures for information extraction or data mining. We have compiled a lexicon of biomedical words (conserved patterns/ potential motifs) which has the combination of only 20 alphabets of amino acids. The remaining 6 letters of the English alphabets (B, J, O, U, X, Z) are treated as invalid amino acid characters (to our context), We have jumbled the 6 letters for the sake of usage and convenience and termed as 'JUZBOX' and these characters were filtered in the biomedical lexicon.