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. The purified bacterial phosphatase was subjected to mass spectrometric analysis, and the identity of constructed sequence was analyzed using peptide mass fingerprint. The 3-D structure of protein was elucidated using homology modeling, while its stability was assessed using Ramachandran plot, VERIFY 3D, and PROCHECK. The bacterium produced an extracellular phosphatase of zone diameter 15 ± 0.8 mm on screening medium within 24 h of incubation. This bacterial phosphatase was highly specific towards sodium phytate as it yielded the lowest Km value of 299.50 ± 4.95 µM compared to other phosphorylated substrates. The activity was effectively stimulated in the presence of zinc, magnesium, and manganese ions thereby showing its PTP-like behavior. The phosphatase showed a molecular mass of 43 kDa, and the corresponding M/Z ratio data yielded 46% query coverage to Bacillus subtilis (3QY7). This showed a 61.1% sequence similarity to Ligilactobacillus ruminis (WP_046923835.1). The final sequence construct based on these bacteria showed a conserved motif "HCHILPGIDD" in their active site. In addition, homology modeling showed a distorted Tim barrel structure with a trinuclear metal center. The final model after energy minimization showed 90.9% of the residues in the favorable region of Ramachandran's plot. This structural information can be used in genetic engineering for improving the overall stability and catalytic efficiency of probiotic bacterial phosphatases.

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. The ideas discussed will be useful both for predicting toxicity and for de-risking leads through optimization.

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. Recurrent neural network-based generative models have demonstrated application in low-data drug discovery, fragment-based drug design and in lead optimization. AREAS COVERED: In this review, we have provided an overview of recurrent neural network models and their variants for molecule generation with recent examples. The input representation of molecules as SMILES and molecular graphs have been discussed. The evaluation benchmarks and metrics used in generative neural network models are also highlighted. For this, ScienceDirect, Web of Science, and Google Scholar databases were searched with the article's keywords and their combinations to retrieve the most relevant and up-to-date information. EXPERT OPINION: The simplicity of SMILES notation makes it suitable for training a sequence-based model such as a recurrent neural network. However, models that could be trained on molecular graphs to generate molecular structures which could be synthesized could open new possibility for valid molecule generation and synthetic feasibility.

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. This review brings out the best possible applications of melezitose and present in the form of a mnemonic to remember this forgotten sugar.

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. Fermented bamboo shoots form the niche for many microorganisms, and this confers positive effects and advantages in many ways. These magical shoots have tremendous health benefits like anti-cancer, anti-oxidant, anti-aging, cardioprotective, weight loss, probiotics, to name a few. Apart from health benefits, fermented bamboo shoots form important functional foods and have industrial and economical values. Though these are commonly found and started in the tribal area, and local markets, today, they are valuable all around the world, as popular as gold. Hence, fermented bamboo shoots are referred as "green gold" of India. This review briefs about various health benefits, advantages, disadvantages, future scope, and finally the economic values of fermented bamboo shoots, the "green gold" of the twenty-first century.

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. Therefore, in this study, Streptococcus thermophilus 2412 based phytase stability was assessed at higher temperatures up to 90 °C. This was followed by probiotic validation of the same bacterium in an in vitro intestinal model. Bacterial phytase showed thermostability up to 70 °C with a recorded activity of 9.90 U. The bacterium was viable in the intestinal lumen as indicated by the cell count of 6.10 log(CFU/mL) after 16 h. It also showed acid tolerance with a stable cell count of 5.01 log(CFU/mL) after 16 h of incubation at pH 2. The bacterium displayed bile tolerance yielding a cell count of 6.36 log(CFU/mL) in the presence of 0.3% bile. Bacterial susceptibility was observed toward all tested antibiotics with a maximum zone of 20 mm against clindamycin. The maximum antagonistic activity was observed against Staphylococcus aureus, Serratia marcescens, and Escherichia coli with inhibition zone diameters up to 10 mm. The above characteristics prove that S. thermophilus 2412 can be used as an effective phytase-producing poultry probiotic.

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. In this review, we discuss about machine-learning and deep-learning models used in virtual screening to improve drug-target interaction (DTI) prediction. We also highlight current knowledge and future directions to guide further development in this field.

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 Streptococcus thermophilus, Sporosarcina pasteurii, Sporosarcina globispora, and Sporosarcina psychrophila using known probiotic bacterium, Lactobacillus helveticus 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 3.125 mM and 12.5 mM. These bacteria demonstrated significantly higher (p < 0.05) phosphate liberation (up to 387 µM) due to better phytase activity in the production medium, when compared to the growth medium (339 µM). The phytase activity showed a steady increase in phosphate liberation up to 150 min after which it became constant. This trend is observed for the selected bacteria at pH 5, 6 and 7. However, the liberation of phosphates showed no significant difference (p > 0.05) at the tested pH. Among the analyzed bacteria, the members of the genus Sporosarcina showed better phytate degradation when compared to S. thermophilus. The proposed model can be extended to analyze any extracellular enzymes produced by gut microbes.

In Silico 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. Vpu and tetherin connect through their transmembrane (TM) domains, culminating into events leading to tetherin degradation by recruitment of ß-TrCP2. However, mutations in the TM domains of both proteins are reported to act as a resistance mechanism to Vpu countermeasure impacting tetherin's sensitivity towards Vpu but retaining its antiviral activity. Our study illustrates the binding aspects of blood-derived, brain-derived, and consensus HIV-1 Vpu with tetherin through protein-protein docking. The analysis of the bound complexes confirms the blood-derived Vpu-tetherin complex to have the best binding affinity as compared to other two. The mutations in tetherin and Vpu are devised computationally and are subjected to protein-protein interactions. The complexes are tested for their binding affinities, residue connections, hydrophobic forces, and, finally, the effect of mutation on their interactions. The single point mutations in tetherin at positions L23Y, L24T, and P40T, and triple mutations at {L22S, F44Y, L37I} and {L23T, L37T, T45I}, while single point mutations in Vpu at positions A19H and W23Y and triplet of mutations at {V10K, A11L, A19T}, {V14T, I18T, I26S}, and {A11T, V14L, A15T} have revealed no polar contacts with minimal hydrophobic interactions between Vpu and tetherin, resulting in reduced binding affinity. Additionally, we have explored the aggregation potential of tetherin and its association with the brain-derived Vpu protein. This work is a possible step toward an understanding of Vpu-tetherin interactions.

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. Therefore, spore-forming bacteria belonging to Sporosarcina genus such as pasteurii, globispora, and psychrophila were assessed for probiotic characteristics such as biofilm formation, intestinal adhesion, acid and bile tolerance, antibiotic sensitivity, and anti-pathogenic activity. This ensures bacterial viability under gastrointestinal conditions and enabled the same to colonize effectively in the intestinal lumen (in vitro). The bacterial cell counts ranging from 6.59 to 6.91 log(CFU/mL) was observed for Sporosarcina spp. after 16 h. This indicated that there is no significant difference in the cell counts (P-value = 0.90). The cell counts of Sporosarcina spp. ranging from 5.57 to 5.93 log(CFU/mL) displayed strong acid tolerance at pH 2. They were also viable at higher bile (0.5%) concentration. Among the Sporosarcina spp., pasteurii showed better tolerance (6.90 log(CFU/mL)) even after 16 h. Among the selected bacteria, Sporosarcina psychrophila was more susceptible to teicoplanin and meropenem with an inhibition zone of 30 mm. Maximum antagonistic activity was observed against Serratia marcescens (with inhibition zone up to 15 mm). Our results suggest that bacteria belonging to Sporosarcina genus possess all the required characteristics to be used as potential poultry probiotics.

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

Microbial degradation of myo-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 Sporosarcina spp. pasteurii, globiospora, psychrophila, Streptococcus thermophilus and Saccharomyces boulardii. These microbes were screened for phytase production under laboratory conditions. The specificity of the enzyme was tested for various phosphorylated substrates such as sodium phytate (IP6), sodium hexametaphosphate, phenyl phosphate, α-d-glucose-6 phosphate, inosine 5' monophosphate and pyridoxal 5' phosphate. These enzymes were highly specific to IP6. The influence of modulators such as phytochemicals and metal ions on the enzymatic activity was assessed. These modulators in different concentrations had varying effect on microbial phytases. Calcium (in optimal concentration of 0.5 M) played an important role in enzyme activation. The enzymes were then characterized based on their molecular weight 41~43 kDa. The phytase-producing microbes were assessed for IP6 degradation in a simulated intestinal setup. Among the selected microbes, Sporosarcina globiospora hydrolyzed IP6 effectively, as confirmed by colorimetric time-based analysis.

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. Few viral proteins like gp-120 are known to be involved in aggregation and enhancement of viral infectivity while comprehending the neurotoxic role of some other proteins is still underway. In the current study, amyloidogenic potential of HIV-1 Vpu protein from brain isolate is investigated through computational approaches. The aggregation propensity of brain derived HIV-1 Vpu was assessed by several amyloid prediction servers that projected the region 4-35 to be amyloidogenic. The protein structure was modeled and subjected to 70 ns molecular dynamics (MD) simulation to investigate the transformation of α-helical conformation of the predicted aggregate region into ß-sheet, proposing the protein's ability to initiate fibril formation that is central to amyloidogenic proteins. The structural features of brain derived HIV-1 Vpu were consistent with the in silico amyloid prediction results that depicts the conformational change in the region 8-28 of which residues Ala8, Ile9, Val10, Ala19, Ile20 and Val21 constitutes ß-sheet formation. The α-helix/ß-sheet discordance of the predicted region was reflected in the simulation study highlighting the possible structural transition associated with HIV-1 Vpu protein of brain isolate.

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). Cutaneous leishmaniasis causes an ulcer on exposed parts of the body and it was estimated that 0.7-1.3 million cases occur worldwide annually. Mucocutaneous leishmaniasis leads to destruction of mucous membranes in various parts of the body and it was reported that it occurs widely in South America. VL is a deadly disease and it is characterized by various symptoms, such as anemia, fever, fatigue and weight loss. The WHO estimated that 200,000-400,000 cases per annum of VL occur worldwide. Although different drugs and drug combinations are used for leishmaniasis, US FDA-approved drugs are limited. Miltefosine is the only drug approved for all forms of leishmaniasis and AmBisome(®) is approved for VL. Moreover, the drugs used for leishmaniasis have severe side effects. The article summarizes the patents filed between January 2010 and June 2013 for antileishmanial activity. The article covers only the chemical agents and excludes the vaccines and the peptides. A large number of compounds are filed for antileishmanial activity annually, but only a few are more potent than reference drugs such as miltefosine, pentamidine and metronidazole. In addition, most of the compounds are not as efficient as amphotericin B. Therefore, there is a need for novel compounds that are not only potent than the FDA-approved AmBisome and miltefosine, but are also less toxic and more cost effective in humans. This article provides an eclectic compilation of different classes of compounds that are active against amastigotes (the protozoa form found in humans) for the treatment of leishmaniasis.

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. Undoubtedly, the generation of biomedical words from protein sequence using JUZBOX have applications specific for functional annotation. AVAILABILITY: JUZBOX is available freely at http://www.spices.res.in/juzbox.