Ashish Runthala

SR University · School of Sciences and Humanities

The field of enzyme design methodologies has emerged as a promising avenue for enhancing enzymatic yield, enabling the optimization of enzyme performance for various industrial and scientific applications. These methodologies encompass a range of computational and experimental techniques aimed at tailoring enzyme properties, such as activity, selec...

Introduction With more than 70,000 unique compounds indexed in the Dictionary of Natural Products database, terpenes and their various derivatives are one of the largest and structurally most diverse categories of natural chemicals [1]. These molecules serve a variety of functions, ranging from protein prenylation, mediating antagonistic/symbiotic...

Humanity has been battling with tuberculosis (TB) for a long period, and despite the availability of drugs well-known to act against the deadly microbe, the menace is still very far from reaching its end. Moreover, problems related to TB chemotherapy, such as lengthy treatment periods leading to poor patient compliance, increasing drug resistance,...

Pancreatic lipase is one of the crucial lipolytic enzymes of the gut that actively facilitates the digestion and absorption of the dietary triglycerides and cholesteryl esters. Although it has been deemed as one of the most reliable targets for the treatment of obesity and/or dyslipidemia, to date, orlistat is the only known FDA-approved, effective...

This book provides a meticulous view on methodological drug discovery and development insights from bench to bedside. The current book threads almost each step encompassing drug the discovery and development of a molecule. The chapters focus on computational modus operandi, pharmacological optimization approaches, modern high-throughput screening m...

1 0 1 1 Transaminases, enzymes facilitating amino group transfers, are divided into four subfamilies: D-alanine transaminase (DATA), L-selective Branched chain aminotransferase (BCAT), 4-amino-4-deoxychorismate lyase (ADCL), and R-selective aminotransferase (RATA). RATA enzymes are particularly valuable in biocatalysis for synthesizing chiral amine...

A phylogenetic tree commonly represents evolutionary relationships within a set of protein sequences. Various methods and strategies have been used to improve the accuracy of phylogenetic trees, but their capacity to derive a biologically credible relationship appears to be overestimated. Although the quality of the protein sequence alignment and t...

Background: Reportedly, lifestyle diseases are the chronic non-communicable diseases that have substantially drawn the global attention. Indeed, the global mortality is expected to rise up to 70% by 2030 due to the influence of the lifestyle diseases. Regular physical activity, healthy diet, and refraining from the substance abuse remain the best r...

SARS-CoV-2 is the etiological agent liable for the viral pneumonia outbreak since later 2019 that originated in Wuhan. It has been declared as a pandemic by the World Health Organization. The virus is mainly spread from person to person mostly through airborne, fomite, contact, and droplet from the infected persons. Although there are latest vaccin...

The milk of mammals is a complex fluid mixture of various proteins, minerals, lipids, and other micronutrients that play a critical role in providing nutrition and immunity to newborns. Casein proteins together with calcium phosphate form large colloidal particles, called casein micelles. Caseins and their micelles have received great scientific in...

This special issue is dedicated to the cover the major research and innovations happening in the field of enzyme design as well as catalytic enhancement of the product yield. The papers presented in this special issue will cover various topics connected with genetic engineering, production processes and bioprocessing. Topics: Protein engineering,...

Diabetes is one of the most common chronic diseases that contribute significantly to global mortality. Effective glucose-sensing platforms might allow for an improved monitoring of disease progression, leading to a better health management. Optical sensors based on smart materials, particularly those that respond to external stimuli, have recently...

Dear Researcher, We are currently working as a guest editor for the special issue of this high-impact JCR-Q1 Journal (Impact Factor: 6.064). This special issue is dedicated to the cover the major research and innovations happening in the field of enzyme design as well as catalytic enhancement of the product yield. The papers presented in this speci...

Background and aim The insulin resistance-mediated abnormal gluconeogenesis when exceeds a given threshold culminates in type 2 diabetes mellitus (T2DM).This induces severe cellular oxidative stress that may eventually facilitate typical neoplastic transformations.This narrative review aims to portray some of the plausible key mechanistic links bri...

Terpenoids form a large pool of highly diverse organic compounds possessing several economically important properties, including nutritional, aromatic, and pharmacological properties. The 1-deoxy-D-xylulose 5-phosphate (DXP) pathway’s end enzyme, nuclear distribution protein (NudF), interacting with isopentenyl pyrophosphate (IPP) and dimethylallyl...

Background Terpenoids form a large pool of highly diverse organic compounds possessing several economically important properties, including nutritional, aromatic, and pharmacological properties. The DXP pathway’s end enzyme, nuclear distribution protein (NudF), interacting with isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP)...

Recent advancements in medicinal research have identified several antiviral and anticancer terpenoids that are usually deployed as a source of flavor, fragrances and pharmaceuticals. Under the current COVID-19 pandemic conditions, natural therapeutics with least side effects are the need of the hour to save the patients, especially, which are pre-a...

To increase the expression of a native/foreign plant/bacterial gene, the complete network of cis-elements must be excavated to increase its biosynthetic yield, especially under industrial stress conditions. For selecting the best set of cis-elements for a foreign gene and aiding the workflow of researchers, often untrained in bioinformatics methodo...

Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyses the bio-logical reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts including drugs and chemicals, we have been striving to design the industrially useful enzyme molecules with hig...

Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts including drugs and chemicals, we have been striving to design the industrially useful enzyme molecules with high...

For drawing an evolutionary relationship among several protein sequences, the phylogenetic tree is usually constructed through maximum likelihood-based algorithms. To improve the accuracy of these methodologies, many parameters like bootstrap methods, correlation coefficient and residue-substitution models are presumably over-ranked to derive biolo...

Protein structural information is essential for the detailed mapping of a functional protein network. For a higher modelling accuracy and quicker implementation, template-based algorithms have been extensively deployed and redefined. The methods only assess the predicted structure against its native state/template and do not estimate the accuracy f...

Background: To achieve a high yield of terpenoid-based therapeutics, 1-deoxy-d-xylulose-5-phosphate (DXP) pathway has been significantly exploited for the production of downstream enzymes. The DXP synthase (DXS) enzyme, the initiator of this pathway, is pivotal for the convergence of carbon flux, and is computationally studied well for the industri...

Protein structural information is essential for the detailed mapping of a functional protein network. For a higher modelling accuracy and quicker implementation, template based algorithms have been extensively deployed and redefined. The methods only assess the predicted structure against its native state/template, and do not estimate the accuracy...

lactalbumin-Oleic acid complex derived from milk is well known to have anti-cancer properties in many diverse mammalian species including humans, goats and cows. The objective of the current study is to see if α-lactalbumin present in camel's milk too can serve as a potential anti-cancer molecule in its complex form. A comparative evaluation of α-l...

Terpene or terpenoid or isoprenoid represents the largest class of secondary metabolites and has a variety of applications in food, fragrance, and pharmaceutical industry. Recent advancements and extensive research analysis on various cell lines and animal models have recognized their anticancer potential. To date plants are the major sources of su...

An analysis of the ATP-dependent RNA helicase using known functionally close analogs help disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active site residues to infer function and establish role. The human protein q96c10.1 i...

Extra Cytoplasmic Function (ECF) σ factor/regulatory protein (anti-σ factor) pairs govern environment mediated changes in gene expression in bacteria. The release of the ECF σ factor from an inactive σ/anti-σ factor complex is triggered by specific environmental stimuli. The free σ factor then associates with the RNA polymerase and drives the expre...

In contrast to ab-initio protein modelling methodologies, comparative modelling is considered as the most popular and reliable algorithm to model protein structure. However, the selection of the best set of templates is still a major challenge. An effective template-ranking algorithm is developed to efficiently select only the reliable hits for pre...

Summarized tabular results: Comparative accuracy of our predicted CASP8, CASP9 and CASP10 TBM target targets models against the top-model predicted during the tests.. Our algorithmic accuracy is much higher than the top10 modelling algorithms for most of these TBM targets..

Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitates the computer-aided directed evolution of enzymes. Our initial work (Amrein et al., IUCrJ 4:50–64, 2017) presented a pedagogical example of...

Salinity stress adversely affects the plant growth and is a major constraint to agriculture. In the present study, we studied the role of plant growth promoting rhizobacterium (PGPR) Enterobacter cloacae SBP-8 possessing ACC deaminase activity on proteome profile of wheat (Triticum aestivum L.) under high salinity (200 mM NaCl) stress. The aim of s...

The total protein recorded in the T-1 treatment (uninoculated control plants treated with and without salt stress), T-2 (bacterial inoculated plants and their uninoculated control plants), and T-3 treatment (bacterial inoculated plants treated with salt stress and bacterial inoculated control plants grown without salt stress). (XLSX)

Near-native protein structure prediction through Template Based Modelling (TBM) has been a major realistic goal of structural biology for several years. The TBM algorithms require the best-set of templates for a target protein sequence to maximally cover it and construct its correct topology. However, the accuracy of such prediction algorithms suff...

Structural and functional characterization of protein sequences is one of the important areas of biological research. Currently, a small number of experimentally solved protein structures exist in Protein Data Bank (PDB) in comparison to their considerably higher count of sequence available in UniProtKB/Swiss-Prot. Ambient template-based modelling...

Template based protein modelling is currently the most accurate as well as trustworthy method for predicting the correct protein conformations to bridge the constantly increasing gap between the number of experimentally solved protein structures and the count of protein sequences. Our best knowledge based prediction algorithms employing the templat...

Evolution, often considered with large sample size, positive natural selection drives the path of improvement in biological sequence information. Evolution in proteins is much more complex than in DNA. Factors assisting the evolutionary rate and models are focused in reference to proteins to emphasize their major functional role in evolution. Envir...

Mutation in a single nucleotide of a gene has the potential to change the structure and/or function of its protein. Albeit simply saying, it is not observed to be a general phenomenon. The effect of mutation is primarily determined by the stereochemical nature of the amino acid which has replaced the previous amino acid, resulting in the residue lo...

Protein structure prediction is the major goal to match up the count of known protein sequences and solved protein structures. Current template based modelling methodologies (TBM) rely on selection of structural folds or evolutionary related templates from already solved experimental structures. Even when the first predicted model conformation from...

Correct mapping of functional network ofprotein sequences is one of the major issues in biological research. Detailed knowledge of high resolution protein conformations is the key to it. But still, there is a huge sequence-structure gap between the available number of protein sequences and the known count of experimentally solved structures. Becaus...

Health risk of obesity is a heavily growing concern for societies across the globe, as it is the root cause of several lethal diseases, for which the cure is highly expensive. I tried an innovative approach with some formulations and calculations, and it has shown excellent results.The work is intended to explore the efficacy of the judiciously pra...

Evolution has often been interpreted as the positive natural selection, paving the path for adaptive improvement in biological genetic information. Evolution yielding functionally adapted protein molecules is much more complex than DNA. Constraints mediating the rate, path and altered convergence of functionally evolved proteins are justified to...

Functional characterization of proteins being one of the major issues in molecular biology is still unsolved due to several resource and technical limitations of experimental structure determination methods. A suitable methodology for accurate prediction of protein confirmations simply from sequence is therefore emerging as the primary modeling goa...

The televisions today are all showing the two dimensional display. And we are heading on for increasing the pixels, both in computer monitors and Television sets, for increasing the resolution. Looking forward for implementing the third dimensional display in existing setup of televisions, without adding additional devices will be a revolution i...

Protein structure prediction (PSP) is one of the biggest challenges of Structural Genomics. Protein modeling algorithms, aiming at bridging the big gap between the count of solved structures and known protein sequences, are still not successful. Our algorithms are still limited in their usage and application domain. Major problems obstructing the a...

Fermentation products are indigenous to many civilizations, and they have been produced by industries since a long time. Saccharomyces cerevisiae S288C (commonly known as baker's yeast) is the strain mainly used in the Glucose based fermentation industries. We have seen the use of same yeast strain at different places with different Phenotypic Cons...

Alpha Trans Inducing Factor (a-TIF) is a herpes simplex virus type 1 (HSV-1) virion tegument protein present in the tegument layer between the capsid and the envelope, in association with cellular proteins and trans-activated viral activities. a-TIF stimulates the transcription of HSV-1 Immediate Early genes during lytic virus replication. The pres...

Alzheimer’s disease is a fatal brain disorder. It is progressive cognitive disease as it destroys neurons, causing problems with memory, behavior, and finally hampers work. The role of amyloid plaques in the disease is mostly about the β-amyloid protein, which is part of much larger protein called Amyloid precursor protein (APP). Many drug targ...

The recent wave of misuse and the hacking attacks on some of the Web's most established and popular sites proves that, like flu shots, last year's protection does little against this year's threats. And it's everyone's responsibility to avoid being a carrier of infection. So, knowing the things is the better option to prevent those things to hap...

Helicobacter pylori is a Gram-negative, microaerophilic bacterium that inhibits various areas of the stomach and duodenum. It causes a chronic low-level inflammation of the stomach lining and is strongly linked to the development of duodenal and gastric ulcers and stomach cancer. To better understand adaptive mechanisms utilized by H.pylori wit...

Diseases are persistently getting diversified, evolved and thus require rapid vaccine development methodologies. Complex archaic methods require painstaking efforts over a larger time span. In silico methods are utilized these days to screen potent antigens. This approach paves a future way to reduce the number of wet-lab experiments. Its importanc...

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