Tuneable quantised conductance memory states in TiO2based resistive switching devices in crossbar geometry for high density memory applications.

The tunability and controllability of conductance quantization mediated multilevel resistive switching (RS) memory devices, fabricated in crossbar geometry can be a promising alternative for boosting storage density. Here, we report fabrication of Cu/TiO2/Pt based RS devices in 8 × 8 crossbar geometry, which showed reliable bipolar RS operations. The crossbar devices showed excellent spatial and temporal variability, time retention and low switching voltage (<1 V) and current (∼100µA). Furthermore, during the reset switching, highly repeatable and reliable integral and half-integral quantized conductance (QC) was observed. The observed QC phenomenon was attributed to the two dimensional confinement of electrons as lateral width of the conducting filament (CF) matches the fermi wavelength. The magnitude and number of the QC steps were found to increase from ∼2.5 to 12.5 and from 5 to 18, respectively by increasing the compliance current (IC) from 50 to 800µA which also increased the diameter of the CF from ∼1.2 to 3.3 nm. The enhancement in both number and magnitude of QC states was explained using electrochemical dissolution mechanism of CF of varying diameter. A thicker CF, formed at higherIC, undergoes a gradual rupture during reset process yielding a greater number of QC steps compared to a thinner CF. The realisation of QC states in the crossbar Cu/TiO2/Pt device as well asICmediated tunability of their magnitude and number may find applications in high-density resistive memory storage devices and neuromorphic computing.

Effectiveness of Immune Checkpoint Inhibitors in Various Tumor Types Treated by Low, Per-Weight, and Conventional Doses at a Tertiary Care Center in Mumbai.

PURPOSE: The cost of immune checkpoint inhibitors (ICIs) limits their accessibility to a small number of patients with cancer in low- and middle-income countries. Early-phase clinical trials have shown target inhibition and high activity at doses lower than those registered and evaluated in clinical trials. Here, we report everyday experience of using ICIs in 100 Indian patients, many of whom received lower doses of ICIs. METHODS: Consecutive patients who received at least one dose of an ICI irrespective of tumor type at a tertiary care hospital in Mumbai, India, that was able to access ICIs for its patients were enrolled. The objectives were to study the doses used over a 3-year time period, and the effectiveness of therapy, assessed primarily by the overall response rate (ORR), overall survival (OS), and progression-free survival were secondary end points. RESULTS: Twenty-five patients were treated with conventional doses of ICIs, 29 patients received lower doses per body weight, and 46 patients received low-dose treatment. The median number of cycles received was 5 (range, 1-28). Seventy-eight patients received ICIs in a palliative setting. The median follow-up time was 10.2, 9.8, and 3.9 months for those receiving fixed approved dosing, per body weight dosing, and low-dose treatment, respectively. There was a trend with time to prescribe lower doses. Response evaluation was available for 92 patients. Twenty-one (five-adjuvant and 16-palliative) patients received ICIs only. The ORR did not differ statistically among different dosing groups, but comparisons are confounded by inclusion of different ICIs, different tumor sites, and concurrent treatments. The median OS was 6.8 (range, 4.6-9.0) months. CONCLUSION: Adoption of per-body weight and lower dosing of ICIs appears to give acceptable outcomes. Lower dosing can improve access and timely delivery of ICIs in low- and middle-income countries.

Deciphering the mannose transfer mechanism of mycobacterial PimE by molecular dynamics simulations.

Phosphatidyl-myo-inositol mannosides (PIMs), Lipomannan (LM), and Lipoarabinomannan (LAM) are essential components of the cell envelopes of mycobacteria. At the beginning of the biosynthesis of these compounds, phosphatidylinositol (PI) is mannosylated and acylated by various enzymes to produce Ac1/2PIM4, which is used to synthesize either Ac1/2PIM6 or LM/LAM. The protein PimE, a membrane-bound glycosyltransferase (GT-C), catalyzes the addition of a mannose group to Ac1PIM4 to produce Ac1PIM5, using polyprenolphosphate mannose (PPM) as the mannose donor. PimE-deleted Mycobacterium smegmatis (Msmeg) showed structural deformity and increased antibiotic and copper sensitivity. Despite knowing that the mutation D58A caused inactivity in Msmeg, how PimE catalyzes the transfer of mannose from PPM to Ac1/2PIM4 remains unknown. In this study, analyzing the AlphaFold structure of PimE revealed the presence of a tunnel through the D58 residue with two differently charged gates. Molecular docking suggested PPM binds to the hydrophobic tunnel gate, whereas Ac1PIM4 binds to the positively charged tunnel gate. Molecular dynamics (MD) simulations further demonstrated the critical roles of the residues N55, F87, L89, Y163, Q165, K197, L198, R251, F277, W324, H326, and I375 in binding PPM and Ac1PIM4. The mutation D58A caused a faster release of PPM from the catalytic tunnel, explaining the loss of PimE activity. Along with a hypothetical mechanism of mannose transfer by PimE, we also observe the presence of tunnels through a negatively charged aspartate or glutamate with two differently-charged gates among most GT-C enzymes. Common hydrophobic gates of GT-C enzymes probably harbor sugar donors, whereas, differently-charged tunnel gates accommodate various sugar-acceptors.

Putative staphylococcal enterotoxin possesses two common structural motifs for MHC-II binding.

Staphylococcus aureus has become a significant cause of health risks in humankind. Staphylococcal superantigens (SAgs) or enterotoxins are the key virulent factors that can exhibit acute diseases to severe life-threatening conditions. Recent literature reports S. aureus has steadily gained new enterotoxin genes over the past few decades. In spite of current knowledge of the established SAgs, several questions on putative enterotoxins are still remaining unanswered. Keeping that in mind, this study sheds light on a putative enterotoxin SEl26 to characterize its structural and functional properties. In-silico analyses indicate its close relation with the conventional SAgs, especially the zinc-binding SAgs. Additionally, important residues that are vital for the T-cell receptor (TcR) and major histocompatibility complex class II (MHC-II) interaction were predicted and compared with established SAgs. Besides, our biochemical analyses exhibited the binding of this putative enterotoxin with MHC-II, followed by regulating pro-inflammatory and anti-inflammatory cytokines.

Crystal structure of a thiolase from Archaeal Pyrococcus furiosus and its in silico functional annotation.

In most of the eukaryotes and archaea, isopentenyl pyrophosphate (IPP) and dimethyl allyl pyrophosphate (DMAPP) essential building blocks of all isoprenoids synthesized in the mevalonate pathway. Here, the first enzyme of this pathway, acetoacetyl CoA thiolase (PFC_04095) from an archaea Pyrococcus furiosus is structurally characterized. The crystal structure of PFC_04095 is determined at 2.7 Å resolution, and the crystal structure reveals the absence of catalytic acid/base cysteine in its active site, which is uncommon in thiolases. In place of cysteine, His285 of HDAF motif performs both protonation and abstraction of proton during the reaction. The crystal structure shows that the distance between Cys83 and His335 is 5.4 Å. So, His335 could not abstract a proton from nucleophilic cysteine (Cys83), resulting in the loss of enzymatic activity of PFC_04095. MD simulations of the docked PFC_04095-acetyl CoA complex show substrate binding instability to the active site pocket. Here, we have reported that the stable binding of acetyl CoA to the PFC_04095 pocket requires the involvement of three protein complexes, i.e., thiolase (PFC_04095), DUF35 (PFC_04100), and HMGCS (PFC_04090).

Staphylococcal superantigen-like protein 10 enhances the amyloidogenic biofilm formation in Staphylococcus aureus.

Staphylococcus aureus is a highly infectious pathogen that represents a significant burden on the current healthcare system. Bacterial attachment to medical implants and host tissue, and the establishment of a mature biofilm, play an important role in chronic diseases such as endocarditis, osteomyelitis and wound infections. These biofilms decrease bacterial susceptibility to antibiotics and immune defences, making the infections challenging to treatment. S. aureus produces numerous exotoxins that contribute to the pathogenesis of the bacteria. In this study, we have identified a novel function of staphylococcal superantigen-like protein 10 (SSL10) in enhancing the formation of staphylococcal biofilms. Biofilm biomass is significantly increased when SSL10 is added exogenously to bacterial cultures, whereas SSL2 and SSL12 are found to be less active. Exogenously added SSL10 mask the surface charge of the bacterial cells and lowers their zeta potential, leading to the aggregation of the cells. Moreover, the biofilm formation by SSL10 is governed by amyloid aggregation, as evident from spectroscopic and microscopic studies. These findings thereby give the first overview of the SSL-mediated amyloid-based biofilm formation and further drive the future research in identifying potential molecules for developing new antibacterial therapies against Staphylococcus aureus.

Rationally Designed Novel Phenyloxazoline Synthase Inhibitors: Chemical Synthesis and Biological Evaluation to Accelerate the Discovery of New Antimycobacterial Antibiotics.

The uncontrolled spread of drug-resistant tuberculosis (DR-TB) clinical cases necessitates the urgent discovery of newer chemotypes with novel mechanisms of action. Here, we report the chemical synthesis of rationally designed novel transition-state analogues (TSAs) by targeting the cyclization (Cy) domain of phenyloxazoline synthase (MbtB), a key enzyme of the conditionally essential siderophore biosynthesis pathway. Following bio-assay-guided evaluation of TSA analogues preferentially in iron-deprived and iron-rich media to understand target preferentiality against a panel of pathogenic and non-pathogenic mycobacteria strains, we identified a hit, i.e., TSA-5. Molecular docking, dynamics, and MMPBSA calculations enabled us to comprehend TSA-5's stable binding at the active site pocket of MbtB_Cy and the results imply that the MbtB_Cy binding pocket has a strong affinity for electron-withdrawing functional groups and contributes to stable polar interactions between enzyme and ligand. Furthermore, enhanced intracellular killing efficacy (8 µg/mL) of TSA-5 against Mycobacterium aurum in infected macrophages is noted in comparison to moderate in vitro antimycobacterial efficacy (64 µg/mL) against M. aurum. TSA-5 also demonstrates whole-cell efflux pump inhibitory activity against Mycobacterium smegmatis. Identification of TSA-5 by focusing on the modular MbtB_Cy domain paves the way for accelerating novel anti-TB antibiotic discoveries.

Isolation and spectral characterisation of bioactives from sea weed Hydrocharis laevigata (Humb. & Bonpl. ex Willd.) Byng & Christenh. - using in silico & high throughput analytical techniques.

This work is the first report dealing with the identification and characterisation of the secondary metabolites of the ethanolic extract of Hydrocharis Laevigata (Humb. & Bonpl. Ex Willd.) Byng & Christenh. The ethanolic extract of H. laevigata was analysed by LCMS& Direct mass spectral analysis which is allowed to identify and Interpreted 6 & 15 compounds. The main constituents were caffeic acid, rosemary acid, Perilic acid, strychnine, hydroxy stearic acid, respectively. The extract further purified by column chromatography 15 fractions was isolated, out of which Perilic acid and strychnine are in high quantities. The structure determination of Perilic acid and strychnine was analysed by FTIR and NMR, respectively. By the molecular docking studies of Perilic acid and strychnine shows active binding energies for antidiabetic activity, respectively. The binding energy was compared with Metformin.

Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study.

MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen, Mycobacterium tuberculosis (Mtb), aiding their survival. Though extensively studied, the mode of action between the antitoxin-toxin and DNA of this family remains largely unclear. Here, the important interactions between MazF7 toxin and MazE7 antitoxin, and how MazE7 binds its promoter/operator region have been studied. To elucidate this, molecular dynamics (MD) simulation has been performed on MazE7, MazF7, MazEF7, MazEF7-DNA, and MazE7-DNA complexes to investigate how MazF7 and DNA affect the conformational change and dynamics of MazE7 antitoxin. This study demonstrated that the MazE7 dimer is disordered and one monomer (Chain C) attains stability after binding to the MazF7 toxin. Both the monomers (Chain C and Chain D) however are stabilized when MazE7 binds to DNA. MazE7 is also observed to sterically inhibit tRNA from binding to MazF7, thus suppressing its toxic activity. Comparative structural analysis performed on all the available antitoxins/antitoxin-toxin-DNA structures revealed MazEF7-DNA mechanism was similar to another TA system, AtaRT_E.coli. Simulation performed on the crystal structures of AtaR, AtaT, AtaRT, AtaRT-DNA, and AtaR-DNA showed that the disordered AtaR antitoxin attains stability by AtaT and DNA binding similar to MazE7. Based on these analyses it can thus be hypothesized that the disordered antitoxins enable tighter toxin and DNA binding thus preventing accidental toxin activation. Overall, this study provides crucial structural and dynamic insights into the MazEF7 toxin-antitoxin system and should provide a basis for targeting this TA system in combating Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.

Targeting Staphylococcal Cell-Wall Biosynthesis Protein FemX Through Steered Molecular Dynamics and Drug-Repurposing Approach.

Staphylococcus aureus-mediated infection is a serious threat in this antimicrobial-resistant world. S. aureus has become a "superbug" by challenging conventional as well as modern treatment strategies. Nowadays, drug repurposing has become a new trend for the discovery of new drug molecules. This study focuses on evaluating FDA-approved drugs that can be repurposed against S. aureus infection. Steered molecular dynamics (SMD) has been performed for Lumacaftor and Olaparib against staphylococcal FemX to understand their binding to the active site. A time-dependent external force or rupture force has been applied to the ligands to calculate the force required to dislocate the ligand from the binding pocket. SMD analysis indicates that Lumacaftor has a high affinity for the substrate binding pocket in comparison to Olaparib. Umbrella sampling exhibits that Lumacaftor possesses a higher free energy barrier to displace it from the ligand-binding site. The bactericidal activity of Lumacaftor and Olaparib has been tested, and it shows that Lumacaftor has moderate activity along with biofilm inhibition potential (MIC value with conc. 128 µg/mL). Pharmacokinetic and toxicology evaluations indicate that Lumacaftor has higher pharmacokinetic potential with lower toxicity. This is the first experimental report where staphylococcal FemX has been targeted for the discovery of new drugs. It is suggested that Lumacaftor may be a potential lead molecule against S. aureus.

Tunable, reversible resistive switching behavior of PVA-zirconia nanocomposite films and validation of the trap-assisted switching mechanism by the selective application of external bias voltages.

Flexible, free-standing polyvinyl alcohol (PVA)-zirconia (mean particle size ∼24 nm) nanocomposite films have been synthesized and their performance as a potential next-generation resistive switching device material has been assessed in this report. The nanocomposite films switch from a high resistive state (HRS) to a low resistive state (LRS) at the SET potential and from LRS to HRS at the RESET potential within the voltage window of 5 V. The origination of trap-assisted SET/RESET potentials has been experimentally validated by analyzing the experimental data and invoking various theoretical models. The impregnation of zirconium dioxide (ZrO2) nanoparticles considerably enhances the interfacial charges facilitated by the formation of dangling bonds. The current (I)-voltage (V) characteristics elucidate how the alteration of free volumetric space in the nanocomposites can modify the SET-RESET potential. This leads to tunable SET/RESET potential, good resistance ratio (∼80), and extensive cycling ability of these PVA-ZrO2 organic flexible nanocomposite films. Herein, we have also investigated the effect of applying external bias voltage (equal to the RESET potential) for possible energy bandgap modification and polymer chain orientation. The impedance spectra differ considerably when the sample is subjected to SET, RESET, and zero voltage bias. The observations have been correlated with the UV-vis absorption spectra and electrical studies. The adopted analysis method and obtained results can open up new avenues for designing and analyzing resistive switching-based random-access memory devices.

Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway.

Secretory proteins are used by pathogenic bacteria to manipulate the host systems and compete with other microorganisms, thereby enabling their survival in their host. Similar to other bacteria, secretory proteins of Mycobacterium tuberculosis also play a pivotal role in evading immune response within hosts, thereby leading to acute and latent tuberculosis infection. Prokaryotes have several classes of bacterial secretory systems out of which the Sec and Tat pathways are the most conserved in Mtb to transport proteins across the cytoplasmic membrane. Here, we report the crystal structure of a secretory protein, Rv0398c determined to 1.9 Å resolution. The protein comprises a core of antiparallel ß sheets surrounded by α helices adopting a unique ß sandwich fold. Structural comparison with other secretory proteins in Mtb and other pathogenic bacteria reveals that Rv0398c may be secreted via the Sec pathway. Our structural and in silico analyses thus provide mechanistic insights into the pathway adopted by Mtb to transport out secretory protein, Rv0398c which will facilitate the invasion to the host immune system.

Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties.

Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long-lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes are considered promising and pertinent mycobacterial drug targets. FadA2 (thiolase) is one of the enzymes involved in Mtb's fatty acid metabolism pathway. FadA2 deletion construct (ΔL136-S150) was designed to produce soluble protein. The crystal structure of FadA2 (ΔL136-S150) at 2.9 Å resolution was solved and analysed for membrane-anchoring region. The four catalytic residues of FadA2 are Cys99, His341, His390 and Cys427, and they belong to four loops with characteristic sequence motifs, i.e., CxT, HEAF, GHP and CxA. FadA2 is the only thiolase of Mtb which belongs to the CHH category containing the HEAF motif. Analysing the substrate-binding channel, it has been suggested that FadA2 is involved in the ß-oxidation pathway, i.e., the degradative pathway, as the long-chain fatty acid can be accommodated in the channel. The catalysed reaction is favoured by the presence of two oxyanion holes, i.e., OAH1 and OAH2. OAH1 formation is unique in FadA2, formed by the NE2 of His390 present in the GHP motif and NE2 of His341 present in the HEAF motif, whereas OAH2 formation is similar to CNH category thiolase. Sequence and structural comparison with the human trifunctional enzyme (HsTFE-ß) suggests the membrane-anchoring region in FadA2. Molecular dynamics simulations of FadA2 with a membrane containing POPE lipid were conducted to understand the role of a long insertion sequence of FadA2 in membrane anchoring.

Role of regional diffusion tensor imaging (DTI)-derived tensor metrics in the evaluation of intracranial gliomas and its histopathological correlation.

Background: The imaging of brain tumours has significantly improved with the use of advanced magnetic resonance (MR) techniques like diffusion tensor imaging (DTI). This study was conducted to analyse the utility of DTI-derived tensor metrics in the evaluation of intracranial gliomas with histopathological correlation and further adoption of these image-data analyses in clinical setting. Methods: A total of 50 patients with suspected diagnosis of intracranial gliomas underwent DTI along with conventional MR examination. The study correlated various DTI parameters in the enhancing part of the tumour and the peritumoral region with the histopathological grades of the intracranial gliomas. Results: The study revealed higher values of Cl (linear anisotropy), Cp (planar anisotropy), AD (axial diffusivity), FA (fractional anisotropy) and RA (relative anisotropy) and lower values of Cs (spherical anisotropy), MD (mean diffusivity) and RD (radial diffusivity) in the enhancing part of the tumour in case of high-grade gliomas. However, in the peritumoral region, the values of Cl, Cp, AD, FA and RA were less whereas values of Cs, MD and RD were more in high-grade gliomas than in the low-grade gliomas. The various cutoff values of these DTI-derived tensor metrics were found to be statistically significant. Conclusion: DTI-derived tensor metrics can be a valuable tool in differentiation between high-grade and low-grade gliomas which might be accepted in clinical practice in near future.

EmergeNet: A novel deep-learning based ensemble segmentation model for emergence timing detection of coleoptile.

The emergence timing of a plant, i.e., the time at which the plant is first visible from the surface of the soil, is an important phenotypic event and is an indicator of the successful establishment and growth of a plant. The paper introduces a novel deep-learning based model called EmergeNet with a customized loss function that adapts to plant growth for coleoptile (a rigid plant tissue that encloses the first leaves of a seedling) emergence timing detection. It can also track its growth from a time-lapse sequence of images with cluttered backgrounds and extreme variations in illumination. EmergeNet is a novel ensemble segmentation model that integrates three different but promising networks, namely, SEResNet, InceptionV3, and VGG19, in the encoder part of its base model, which is the UNet model. EmergeNet can correctly detect the coleoptile at its first emergence when it is tiny and therefore barely visible on the soil surface. The performance of EmergeNet is evaluated using a benchmark dataset called the University of Nebraska-Lincoln Maize Emergence Dataset (UNL-MED). It contains top-view time-lapse images of maize coleoptiles starting before the occurrence of their emergence and continuing until they are about one inch tall. EmergeNet detects the emergence timing with 100% accuracy compared with human-annotated ground-truth. Furthermore, it significantly outperforms UNet by generating very high-quality segmented masks of the coleoptiles in both natural light and dark environmental conditions.

Exploring staphylococcal superantigens to design a potential multi-epitope vaccine against Staphylococcus aureus: an in-silico reverse vaccinology approach.

Staphylococcus aureus is a horrifying bacteria capable of causing millions of deaths yearly across the globe. A major contribution to the success of S. aureus as an ESKAPE pathogen is the abundance of virulence factors that can manipulate the innate and adaptive immune system of the individual. Currently, no vaccine is available to treat S. aureus-mediated infections. In this study, we present in-silico approaches to design a stable, safe and immunogenic vaccine that could help to control the infections associated with the bacteria. Three vital pathogenic secreted toxins of S. aureus, such as staphylococcal enterotoxin A (SEA), staphylococcal enterotoxin B (SEB), Toxic-shock syndrome toxin (TSST-1), were selected using the reverse vaccinology approach to design the multi-epitope vaccine (MEV). Linear B-lymphocyte, cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted from these selected proteins. For designing the multi-epitope vaccine (MEV), B-cell epitopes were joined with the KK linker, CTL epitopes were joined with the AAY linker, and HTL epitopes were joined with the GPGPG linker. Finally, to increase the immune response to the vaccine, a human ß-defensin-3 (hBD-3) adjuvant was added to the N-terminus of the MEV construct. The final MEV was found to be antigenic and non-allergen in nature. In-silico immune simulation and cloning analysis predicted the immune-stimulating potential of the designed MEV construct along with the cloning feasibility in the pET28a(+) vector with the E. coli expression system. This immunoinformatics study provides a platform for designing a suitable, safe and effective vaccine against S. aureus.Communicated by Ramaswamy H. Sarma.

A subtractive proteomics and immunoinformatics approach towards designing a potential multi-epitope vaccine against pathogenic Listeriamonocytogenes.

Listeria monocytogenes is the causative agent of listeriosis, which is dangerous for pregnant women, the elderly or individuals with a weakened immune system. Individuals with leukaemia, cancer, HIV/AIDS, kidney transplant and steroid therapy suffer from immunological damage are menaced. World Health Organization (WHO) reports that human listeriosis has a high mortality rate of 20-30% every year. To date, no vaccine is available to treat listeriosis. Thereby, it is high time to design novel vaccines against L. monocytogenes. Here, we present computational approaches to design an antigenic, stable and safe vaccine against the L. monocytogenes that could help to control the infections associated with the pathogen. Three vital pathogenic proteins of L. monocytogenes, such as Listeriolysin O (LLO), Phosphatidylinositol-specific phospholipase C (PI-PLC), and Actin polymerization protein (ActA), were selected using a subtractive proteomics approach to design the multi-epitope vaccine (MEV). A total of 5 Cytotoxic T-lymphocyte (CTL) and 9 Helper T-lymphocyte (HTL) epitopes were predicted from these selected proteins. To design the multi-epitope vaccine (MEV) from the selected proteins, CTL epitopes were joined with the AAY linker, and HTL epitopes were joined with the GPGPG linker. Additionally, a human ß-defensin-3 (hBD-3) adjuvant was added to the N-terminal side of the final MEV construct to increase the immune response to the vaccine. The final MEV was predicted to be antigenic, non-allergen and non-toxic in nature. Physicochemical property analysis suggested that the MEV construct is stable and could be easily purified through the E. coli expression system. This in-silico study showed that MEV has a robust binding interaction with Toll-like receptor 2 (TLR2), a key player in the innate immune system. Current subtractive proteomics and immunoinformatics study provides a background for designing a suitable, safe and effective vaccine against pathogenic L. monocytogenes.

Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health.

Metabolic activities of the microbial population are important to maintain the balance of almost all the ecosystems on earth. In the human gut environment, these microbial communities play essential roles in digestion and help to maintain biochemical homeostasis by synthesizing several vital metabolic compounds. Imbalance in the microbial abundance and community structure in the human gut microbiota leads to different diseases and metabolic disorders. Studying the metabolic interplay between the microbial consortia within the host environment is the key to exploring the cause behind the development of various diseases condition. However, mapping the entire biochemical characteristic of human gut microbiota may not be feasible only through experimental approaches. Therefore, the advanced systems biology approach, i.e., metagenome-scale community metabolic modelling, is introduced for understanding the metabolic role and interaction pattern of the entire microbiome. This in silico method directly uses the metagenomic information to model the microbial communities, which mimic the metabolic behavior of the human gut microbiome. This review discusses the recent development of metagenome-scale community metabolic model reconstruction tools and their application in studying the inter-link between the human gut microbiome and health. The application of the community metabolic models to study the metabolic profile of the human gut microbiome has also been investigated. Alteration of the metabolic fluxes associated with different biochemical activities in type 1 diabetics, type 2 diabetics, inflammatory bowel diseases (IBD), gouty arthritis, colorectal cancer (CRC), etc., has also been assessed with the metagenome-scale models. Thus, modelling the microbial communities combined with advanced experimental design may lead to novel therapeutic approaches like personalized microbiome modelling for treating human disease.

In-silico identification of critical residues in the mannose-transfer mechanism of phosphatidyl-myo-inositol mannosyltransferase B'.

The complex cellular envelope is one of the major reasons behind the survival in hostile conditions and the emergence of the drug-resisting properties of mycobacteria. Phosphatidyl-myo-inositol hexamannoside (PIM6), Lipomannan (LM), and Lipoarabinomannan (LAM) are important structural constituents of the cell envelope and have roles in modulating host immune functions. Phosphatidyl-myo-inositol (PI) is first mannosylated at the 2-position of the inositol group by phosphatidyl-myo-inositol mannosyltransferase A (PimA) to produce phosphatidyl-myo-inositol monomannoside (PIM1). This PIM1 is then further mannosylated at the 6-position of the inositol group by phosphatidyl-myo-inositol mannosyltransferase B' (PimB') utilizing GDP-mannose as the mannose-donor to synthesize phosphatidyl-myo-inositol dimannoside (PIM2) and GDP. Further mannosylation and acylation on PIM2 produce Ac1/2PIM4, which can then be converted to either Ac1/2PIM6 or LM/LAM. Detailed functional mechanism of how PimB' transfers the mannose sugar to PIM1 is not understood. Using molecular docking, the interactions of PimB' with the substrate PIM1 and the product PIM2 are analyzed here. Molecular dynamics (MD) simulations of PimB' with the substrates and the products were performed for 300ns to find out critical residues involved in the mannose-transfer reaction. Docking and MD analyses indicated the residues R206 and R210 bind both PIM1 and PIM2 and are critical in the mannose-transfer reaction. The residues 120HEVGWSMLPGS130 and 281RTRGGGL288 were involved in the transfer of PIM1 from the active site. The residues 18IGG20, K211, E290, G291, 294IV295, and E298 were also important in the mannosylation reaction. The crucial residues obtained from this study may help design novel drugs against mycobacterial PimB'.

In-silico screening and in-vitro assay show the antiviral effect of Indomethacin against SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the worldwide spread of coronavirus disease 19 (COVID-19), and till now, it has caused death to more than 6.2 million people. Although various vaccines and drug candidates are being tested globally with limited to moderate success, a comprehensive therapeutic cure is yet to be achieved. In this study, we applied computational drug repurposing methods complemented with the analyses of the already existing gene expression data to find better therapeutics in treatment and recovery. Primarily, we identified the most crucial proteins of SARS-CoV-2 and host human cells responsible for viral infection and host response. An in-silico screening of the existing drugs was performed against the crucial proteins for SARS-CoV-2 infection, and a few existing drugs were shortlisted. Further, we analyzed the gene expression data of SARS-CoV-2 in human lung epithelial cells and investigated the molecules that can reverse the cellular mRNA expression profiles in the diseased state. LINCS L1000 and Comparative Toxicogenomics Database (CTD) were utilized to obtain two sets of compounds that can be used to counter SARS-CoV-2 infection from the gene expression perspective. Indomethacin, a nonsteroidal anti-inflammatory drug (NSAID), and Vitamin-A were found in two sets of compounds, and in the in-silico screening of existing drugs to treat SARS-CoV-2. Our in-silico findings on Indomethacin were further successfully validated by in-vitro testing in Vero CCL-81 cells with an IC50 of 12 µM. Along with these findings, we briefly discuss the possible roles of Indomethacin and Vitamin-A to counter the SARS-CoV-2 infection in humans.