Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 16

Search results for: Shanthy Sundaram

16 A Comprehensive Analysis of LACK (Leishmania Homologue of Receptors for Activated C Kinase) in the Context of Visceral Leishmaniasis

Authors: Sukrat Sinha, Abhay Kumar, Shanthy Sundaram


The Leishmania homologue of activated C kinase (LACK) is known T cell epitope from soluble Leishmania antigens (SLA) that confers protection against Leishmania challenge. This antigen has been found to be highly conserved among Leishmania strains. LACK has been shown to be protective against L. donovani challenge. A comprehensive analysis of several LACK sequences was completed. The analysis shows a high level of conservation, lower variability and higher antigenicity in specific portions of the LACK protein. This information provides insights for the potential consideration of LACK as a putative candidate in the context of visceral Leishmaniasis vaccine target.

Keywords: bioinformatics, genome assembly, leishmania activated protein kinase c (lack), next-generation sequencing

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15 Biological Control of Karnal Bunt by Pseudomonas fluorescens

Authors: Geetika Vajpayee, Sugandha Asthana, Pratibha Kumari, Shanthy Sundaram


Pseudomonas species possess a variety of promising properties of antifungal and growth promoting activities in the wheat plant. In the present study, Pseudomonas fluorescens MTCC-9768 is tested against plant pathogenic fungus Tilletia indica, causing Karnal bunt, a quarantine disease of wheat (Triticum aestivum) affecting kernels of wheat. It is one of the 1/A1 harmful diseases of wheat worldwide under EU legislation. This disease develops in the growth phase by the spreading of microscopically small spores of the fungus (teliospores) being dispersed by the wind. The present chemical fungicidal treatments were reported to reduce teliospores germination, but its effect is questionable since T. indica can survive up to four years in the soil. The fungal growth inhibition tests were performed using Dual Culture Technique, and the results showed inhibition by 82.5%. The interaction of antagonist bacteria-fungus causes changes in the morphology of hyphae, which was observed using Lactophenol cotton blue staining and Scanning Electron Microscopy (SEM). The rounded and swollen ends, called ‘theca’ were observed in interacted fungus as compared to control fungus (without bacterial interaction). This bacterium was tested for its antagonistic activity like protease, cellulose, HCN production, Chitinase, etc. The growth promoting activities showed increase production of IAA in bacteria. The bacterial secondary metabolites were extracted in different solvents for testing its growth inhibiting properties. The characterization and purification of the antifungal compound were done by Thin Layer Chromatography, and Rf value was calculated (Rf value = 0.54) and compared to the standard antifungal compound, 2, 4 DAPG (Rf value = 0.54). Further, the in vivo experiments showed a significant decrease in the severity of disease in the wheat plant due to direct injection method and seed treatment. Our results indicate that the extracted and purified compound from the antagonist bacteria, P. fluorescens MTCC-9768 may be used as a potential biocontrol agent against T. indica. This also concludes that the PGPR properties of the bacteria may be utilized by incorporating it into bio-fertilizers.

Keywords: antagonism, Karnal bunt, PGPR, Pseudomonas fluorescens

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14 Isolation and Screening of Antagonistic Bacteria against Wheat Pathogenic Fungus Tilletia indica

Authors: Sugandha Asthana, Geetika Vajpayee, Pratibha Kumari, Shanthy Sundaram


An economically important disease of wheat in North Western region of India is Karnal Bunt caused by smut fungus Tilletia indica. This fungal pathogen spreads by air, soil and seed borne sporodia at the time of flowering, which ultimately leads to partial bunting of wheat kernels with fishy odor and taste to wheat flour. It has very serious effects due to quarantine measures which have to be applied for grain exports. Chemical fungicides such as mercurial compounds and Propiconazole applied to the control of Karnal bunt have been only partially successful. Considering the harmful effects of chemical fungicides on man as well as environment, many countries are developing biological control as the superior substitute to chemical control. Repeated use of fungicides can be responsible for the development of resistance in fungal pathogens against certain chemical compounds. The present investigation is based on the isolation and evaluation of antifungal properties of some isolated (from natural manure) and commercial bacterial strains against Tilletia indica. Total 23 bacterial isolates were obtained and antagonistic activity of all isolates and commercial bacterial strains (Bacillus subtilis MTCC8601, Bacillus pumilus MTCC 8743, Pseudomonas aeruginosa) were tested against T. indica by dual culture plate assay (pour plate and streak plate). Test for the production of antifungal volatile organic compounds (VOCs) by antagonistic bacteria was done by sealed plate method. Amongst all s1, s3, s5, and B. subtilis showed more than 80% inhibition. Production of extracellular hydrolytic enzymes such as protease, beta 1, 4 glucanase, HCN and ammonia was studied for confirmation of antifungal activity. s1, s3, s5 and B. subtilis were found to be the best for protease activity and s5 and B. subtilis for beta 1, 4 glucanase activity. Bacillus subtilis was significantly effective for HCN whereas s3, s5 and Bacillus subtilis for ammonia production. Isolates were identified as Pseudomonas aeruginosa (s1) and B. licheniformis (s3, s5) by various biochemical assays and confirmed by16s rRNA sequencing. Use of microorganisms or their secretions as biocontrol agents to avoid plant diseases is ecologically safe and may offer long term of protection to crop. The above study reports the promising effects of these strains in better pathogen free crop production and quality maintenance as well as prevention of the excessive use of synthetic fungicides.

Keywords: antagonistic, antifungal, biocontrol, Karnal bunt

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13 TiO2/PDMS Coating With Minimum Solar Absorption Loss for Passive Daytime Radiative Cooling

Authors: Bhrigu Rishi Mishra, Sreerag Sundaram, Nithin Jo Varghese, Karthik Sasihithlu


We have designed a TiO2/PDMS coating with 94% solar reflection, 96% IR emission, and 81.8 W/m2 cooling power for passive daytime radiative cooling using Kubelka Munk theory and CST microwave studio. To reduce solar absorption loss in 0.3-0.39 m wavelength region, a TiO2 thin film on top of the coating is used. Simulation using Ansys Lumerical shows that for a 20 m thick TiO2/PDMS coating, a TiO2 thin film of 84 nm increases the coating's reflectivity by 11% in the solar region.

Keywords: passive daytime radiative cooling, disordered metamaterial, Kudelka Munk theory, solar reflectivity

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12 Neural Network Based Decision Trees Using Machine Learning for Alzheimer's Diagnosis

Authors: P. S. Jagadeesh Kumar, Tracy Lin Huan, S. Meenakshi Sundaram


Alzheimer’s disease is one of the prevalent kind of ailment, expected for impudent reconciliation or an effectual therapy is to be accredited hitherto. Probable detonation of patients in the upcoming years, and consequently an enormous deal of apprehension in early discovery of the disorder, this will conceivably chaperon to enhanced healing outcomes. Complex impetuosity of the brain is an observant symbolic of the disease and a unique recognition of genetic sign of the disease. Machine learning alongside deep learning and decision tree reinforces the aptitude to absorb characteristics from multi-dimensional data’s and thus simplifies automatic classification of Alzheimer’s disease. Susceptible testing was prophesied and realized in training the prospect of Alzheimer’s disease classification built on machine learning advances. It was shrewd that the decision trees trained with deep neural network fashioned the excellent results parallel to related pattern classification.

Keywords: Alzheimer's diagnosis, decision trees, deep neural network, machine learning, pattern classification

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11 Virtual Reality Based 3D Video Games and Speech-Lip Synchronization Superseding Algebraic Code Excited Linear Prediction

Authors: P. S. Jagadeesh Kumar, S. Meenakshi Sundaram, Wenli Hu, Yang Yung


In 3D video games, the dominance of production is unceasingly growing with a protruding level of affordability in terms of budget. Afterward, the automation of speech-lip synchronization technique is customarily onerous and has advanced a critical research subject in virtual reality based 3D video games. This paper presents one of these automatic tools, precisely riveted on the synchronization of the speech and the lip movement of the game characters. A robust and precise speech recognition segment that systematized with Algebraic Code Excited Linear Prediction method is developed which unconventionally delivers lip sync results. The Algebraic Code Excited Linear Prediction algorithm is constructed on that used in code-excited linear prediction, but Algebraic Code Excited Linear Prediction codebooks have an explicit algebraic structure levied upon them. This affords a quicker substitute to the software enactments of lip sync algorithms and thus advances the superiority of service factors abridged production cost.

Keywords: algebraic code excited linear prediction, speech-lip synchronization, video games, virtual reality

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10 Aqueous Extract of Argemone Mexicana Roots for Effective Corrosion Inhibition of Mild Steel in HCl Environment

Authors: Gopal Ji, Priyanka Dwivedi, Shanthi Sundaram, Rajiv Prakash


Inhibition effect of aqueous Argemone Mexicana root extract (AMRE) on mild steel corrosion in 1 M HCl has been studied by weight loss, Tafel polarization curves, electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM) and atomic force microscopy (AFM) techniques. Results indicate that inhibition ability of AMRE increases with the increasing amount of the extract. A maximum corrosion inhibition of 94% is acknowledged at the extract concentration of 400 mg L-1. Polarization curves and impedance spectra reveal that both cathodic and anodic reactions are suppressed due to passive layer formation at metal-acid interface. It is also confirmed by SEM micro graphs and FTIR studies. Furthermore, the effects of acid concentration (1-5 M), immersion time (120 hours) and temperature (30-60˚C) on inhibition potential of AMRE have been investigated by weight loss method and electrochemical techniques. Adsorption mechanism is also proposed on the basis of weight loss results, which shows good agreement with Langmuir isotherm.

Keywords: mild steel, polarization, SEM, acid corrosion, EIS, green inhibition

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9 Surfactant Free Synthesis of Magnetite/Hydroxyapatite Composites for Hyperthermia Treatment

Authors: M. Sneha, N. Meenakshi Sundaram


In recent times, magnetic hyperthermia is used for cancer treatment as a tool for active targeting of delivering drugs to the targeted site. It has a potential advantage over other heat treatment because there is no systemic buildup in organs and large doses are possible. The aim of this study is to develop a suitable magnetic biomaterial that can destroy the cancer cells as well as induce bone regeneration. In this work, the composite material was synthesized in two-steps. First, porous iron oxide nano needles were synthesized by hydrothermal process. Second, the hydroxyapatite, were synthesized from natural calcium (i.e., egg shell) and inorganic phosphorous source using wet chemical method. The crystalline nature is confirmed by powder X-ray diffraction analysis (XRD). Thermal analysis and the surface area of the material is studied by Thermo Gravimetric Analysis (TGA), Brunauer-Emmett and Teller (BET) technique. Scanning electron microscope (SEM) images show that the particles have nanoneedle-like morphology. The magnetic property is studied by vibrating sample magnetometer (VSM) technique which confirms the superparamagnetic behavior. This paper presents a simple and easy method for synthesis of magnetite/hydroxyapatite composites materials.

Keywords: iron oxide nano needles, hydroxyapatite, superparamagnetic, hyperthermia

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8 Biocontrol Potential of Trichoderma sp. against Macrophomina phaseolina

Authors: Jayarama Reddy, Anand S., H., Sundaram, Jeldi Hemachandran


Forty two strains of Trichoderma sp. were isolated from cultivated lands around Bangalore and analyzed for their antagonistic potential against Macrophomina phaseolina. The potential of biocontrol agents ultimately lies in their capacity to control pathogens in vivo. Bioefficacy studies were hence conducted using chickpea (Cicer arientum c.v. Annigeri) as an experimental plant by the roll paper towel method. Overall the isolates T6, T35, T30, and T25 showed better antagonistic potential in addition to enhancing plant growth. The production of chitinases to break down the mycelial cell walls of fungal plant pathogens has been implicated as a major cause of biocontrol activity. In order to study the mechanism of biocontrol against Macrophomina phaseolina, ten better performing strains were plated on media, amended with colloidal chitin and Sclerotium rolfsii cell wall extract. All the isolates showed chitinolytic activity on day three as well as day five. Production of endochitinase and exochitinase were assayed in liquid media using colloidal chitin amended broth. Strains T35 and T6 displayed maximum endochitinase and exochitinase activity. Although all strains exhibited cellulase activity, the quantum of enzyme produced was higher in T35 and T6. The results also indicate a positive correlation between enzyme production and bioefficacy.

Keywords: biocontrol, bioefficacy, cellulase, chitinase

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7 Enabling Cloud Adoption Based Secured Mobile Banking through Backend as a Service

Authors: P. S. Jagadeesh Kumar, S. Meenakshi Sundaram


With the increase of prevailing non-traditional rivalry, mobile banking experiences an ever changing commercial backdrop. Substantial customer demands have established to be more intricate as customers request more expediency and superintend over their banking services. To enterprise advance and modernization in mobile banking applications, it is gradually obligatory to deeply leapfrog the scuffle using business model transformation. The dramaturgical vicissitudes taking place in mobile banking entail advanced traditions to exploit security. By reforming and transforming older back office into integrated mobile banking applications, banks can engender a supple and nimble banking environment that can rapidly respond to new business requirements over cloud computing. Cloud computing is transfiguring ecosystems in numerous industries, and mobile banking is no exemption providing services innovation, greater flexibility to respond to improved security and enhanced business intelligence with less cost. Cloud technology offer secure deployment possibilities that can provision banks in developing new customer experiences, empower operative relationship and advance speed to efficient banking transaction. Cloud adoption is escalating quickly since it can be made secured for commercial mobile banking transaction through backend as a service in scrutinizing the security strategies of the cloud service provider along with the antiquity of transaction details and their security related practices.

Keywords: cloud adoption, backend as a service, business intelligence, secured mobile banking

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6 Functionalized Single Walled Carbon Nanotubes: Targeting, Cellular Uptake, and Applications in Photodynamic Therapy

Authors: Prabhavathi Sundaram, Heidi Abrahamse


In recent years, nanotechnology coupled with photodynamic therapy (PDT) has received considerable attention in terms of improving the effectiveness of drug delivery in cancer therapeutics. The development of functionalized single-walled carbon nanotubes (SWCNTs) has become revolutionary in targeted photosensitizers delivery since it improves the therapeutic index of drugs. The objective of this study was to prepare, characterize and evaluate the potential of functionalized SWCNTs using hyaluronic acid and loading it with photosensitizer and to effectively target colon cancer cells. The single-walled carbon nanotubes were covalently functionalized with hyaluronic acid and the loaded photosensitizer by non-covalent interaction. The photodynamic effect of SWCNTs is detected under laser irradiation in vitro. The hyaluronic acid-functionalized nanocomposites had a good affinity with CD44 receptors, and it avidly binds on to the surface of CACO-2 cells. The cellular uptake of nanocomposites was studied using fluorescence microscopy using lyso tracker. The anticancer activity of nanocomposites was analyzed in CACO-2 cells using different studies such as cell morphology, cell apoptosis, and nuclear morphology. The combined effect of nanocomposites and PDT improved the therapeutic effect of cancer treatment. The study suggested that the nanocomposites and PDT have great potential in the treatment of colon cancer.

Keywords: colon cancer, hyaluronic acid, single walled carbon nanotubes, photosensitizers, photodynamic therapy

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5 Application of RS and GIS Technique for Identifying Groundwater Potential Zone in Gomukhi Nadhi Sub Basin, South India

Authors: Punitha Periyasamy, Mahalingam Sudalaimuthu, Sachikanta Nanda, Arasu Sundaram


India holds 17.5% of the world’s population but has only 2% of the total geographical area of the world where 27.35% of the area is categorized as wasteland due to lack of or less groundwater. So there is a demand for excessive groundwater for agricultural and non agricultural activities to balance its growth rate. With this in mind, an attempt is made to find the groundwater potential zone in Gomukhi river sub basin of Vellar River basin, TamilNadu, India covering an area of 1146.6 Sq.Km consists of 9 blocks from Peddanaickanpalayam to Villupuram fall in the sub basin. The thematic maps such as Geology, Geomorphology, Lineament, Landuse, and Landcover and Drainage are prepared for the study area using IRS P6 data. The collateral data includes rainfall, water level, soil map are collected for analysis and inference. The digital elevation model (DEM) is generated using Shuttle Radar Topographic Mission (SRTM) and the slope of the study area is obtained. ArcGIS 10.1 acts as a powerful spatial analysis tool to find out the ground water potential zones in the study area by means of weighted overlay analysis. Each individual parameter of the thematic maps are ranked and weighted in accordance with their influence to increase the water level in the ground. The potential zones in the study area are classified viz., Very Good, Good, Moderate, Poor with its aerial extent of 15.67, 381.06, 575.38, 174.49 Sq.Km respectively.

Keywords: ArcGIS, DEM, groundwater, recharge, weighted overlay

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4 Design and Development of an 'Optimisation Controller' and a SCADA Based Monitoring System for Renewable Energy Management in Telecom Towers

Authors: M. Sundaram, H. R. Sanath Kumar, A. Ramprakash


Energy saving is a key sustainability focus area for the Indian telecom industry today. This is especially true in rural India where energy consumption contributes to 70 % of the total network operating cost. In urban areas, the energy cost for network operation ranges between 15-30 %. This expenditure on energy as a result of the lack of grid power availability highlights a potential barrier to telecom industry growth. As a result of this, telecom tower companies switch to diesel generators, making them the second largest consumer of diesel in India, consuming over 2.5 billion litres per annum. The growing cost of energy due to increasing diesel prices and concerns over rising greenhouse emissions have caused these companies to look at other renewable energy options. Even the TRAI (Telecom Regulation Authority of India) has issued a number of guidelines to implement Renewable Energy Technologies (RETs) in the telecom towers as part of its ‘Implementation of Green Technologies in Telecom Sector’ initiative. Our proposal suggests the implementation of a Programmable Logic Controller (PLC) based ‘optimisation controller’ that can not only efficiently utilize the energy from RETs but also help to conserve the power used in the telecom towers. When there are multiple RETs available to supply energy, this controller will pick the optimum amount of energy from each RET based on the availability and feasibility at that point of time, reducing the dependence on diesel generators. For effective maintenance of the towers, we are planing to implement a SCADA based monitoring system along with the ‘optimization controller’.

Keywords: operation costs, consumption of fuel and carbon footprint, implementation of a programmable logic controller (PLC) based ‘optimisation controller’, efficient SCADA based monitoring system

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3 Early Transcriptome Responses to Piscine orthoreovirus-1 in Atlantic salmon Erythrocytes Compared to Salmonid Kidney Cell Lines

Authors: Thomais Tsoulia, Arvind Y. M. Sundaram, Stine Braaen, Øyvind Haugland, Espen Rimstad, Øystein Wessel, Maria K. Dahle


Fish red blood cells (RBC) are nucleated, and in addition to their function in gas exchange, they have been characterized as mediators of immune responses. Salmonid RBC are the major target cells of Piscineorthoreovirus (PRV), a virus associated with heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon. The activation of antiviral response genesin RBChas previously been described in ex vivo and in vivo PRV-infection models, but not explored in the initial virus encounter phase. In the present study, mRNA transcriptome responses were explored in erythrocytes from individual fish, kept ex vivo, and exposed to purified PRV for 24 hours. The responses were compared to responses in macrophage-like salmon head kidney (SHK-1) and endothelial-like Atlantic salmon kidney (ASK) cells, none of which support PRV replication. The comparative analysis showed that the antiviral response to PRV was strongest in the SHK-1 cells, with a set of 80 significantly induced genes (≥ 2-fold upregulation). In RBC, 46 genes were significantly upregulated, while ASK cells were not significantly responsive. In particular, the transcriptome analysis of RBC revealed that PRV significantly induced interferon regulatory factor 1 (IRF1) and interferon-induced protein with tetratricopeptide repeats 5-like (IFIT9). However, several interferon-regulated antiviral genes which have previously been reported upregulated in PRV infected RBC in vivo (myxovirus resistance (Mx), interferon-stimulated gene 15 (ISG15), toll-like receptor 3 (TLR3)), were not significantly induced after 24h of virus stimulation. In contrast to RBC, these antiviral response genes were significantly upregulated in SHK-1. These results confirm that RBC are involved in the innate immune response to viruses, but with a delayed antiviral response compared to SHK-1. A notable difference is that interferon regulatory factor 1 (IRF-1) is the most strongly induced gene in RBC, but not among the significantly induced genes in SHK-1. Putative differences in the binding, recognition, and response to PRV, and any link to effects on the ability of PRV to replicate remains to be explored.

Keywords: antiviral responses, atlantic salmon, piscine orthoreovirus-1, red blood cells, RNA-seq

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2 Various Shaped ZnO and ZnO/Graphene Oxide Nanocomposites and Their Use in Water Splitting Reaction

Authors: Sundaram Chandrasekaran, Seung Hyun Hur


Exploring strategies for oxygen vacancy engineering under mild conditions and understanding the relationship between dislocations and photoelectrochemical (PEC) cell performance are challenging issues for designing high performance PEC devices. Therefore, it is very important to understand that how the oxygen vacancies (VO) or other defect states affect the performance of the photocatalyst in photoelectric transfer. So far, it has been found that defects in nano or micro crystals can have two possible significances on the PEC performance. Firstly, an electron-hole pair produced at the interface of photoelectrode and electrolyte can recombine at the defect centers under illumination of light, thereby reducing the PEC performances. On the other hand, the defects could lead to a higher light absorption in the longer wavelength region and may act as energy centers for the water splitting reaction that can improve the PEC performances. Even if the dislocation growth of ZnO has been verified by the full density functional theory (DFT) calculations and local density approximation calculations (LDA), it requires further studies to correlate the structures of ZnO and PEC performances. Exploring the hybrid structures composed of graphene oxide (GO) and ZnO nanostructures offer not only the vision of how the complex structure form from a simple starting materials but also the tools to improve PEC performances by understanding the underlying mechanisms of mutual interactions. As there are few studies for the ZnO growth with other materials and the growth mechanism in those cases has not been clearly explored yet, it is very important to understand the fundamental growth process of nanomaterials with the specific materials, so that rational and controllable syntheses of efficient ZnO-based hybrid materials can be designed to prepare nanostructures that can exhibit significant PEC performances. Herein, we fabricated various ZnO nanostructures such as hollow sphere, bucky bowl, nanorod and triangle, investigated their pH dependent growth mechanism, and correlated the PEC performances with them. Especially, the origin of well-controlled dislocation-driven growth and its transformation mechanism of ZnO nanorods to triangles on the GO surface were discussed in detail. Surprisingly, the addition of GO during the synthesis process not only tunes the morphology of ZnO nanocrystals and also creates more oxygen vacancies (oxygen defects) in the lattice of ZnO, which obviously suggest that the oxygen vacancies be created by the redox reaction between GO and ZnO in which the surface oxygen is extracted from the surface of ZnO by the functional groups of GO. On the basis of our experimental and theoretical analysis, the detailed mechanism for the formation of specific structural shapes and oxygen vacancies via dislocation, and its impact in PEC performances are explored. In water splitting performance, the maximum photocurrent density of GO-ZnO triangles was 1.517mA/cm-2 (under UV light ~ 360 nm) vs. RHE with high incident photon to current conversion Efficiency (IPCE) of 10.41%, which is the highest among all samples fabricated in this study and also one of the highest IPCE reported so far obtained from GO-ZnO triangular shaped photocatalyst.

Keywords: dislocation driven growth, zinc oxide, graphene oxide, water splitting

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1 Membrane Permeability of Middle Molecules: A Computational Chemistry Approach

Authors: Sundaram Arulmozhiraja, Kanade Shimizu, Yuta Yamamoto, Satoshi Ichikawa, Maenaka Katsumi, Hiroaki Tokiwa


Drug discovery is shifting from small molecule based drugs targeting local active site to middle molecules (MM) targeting large, flat, and groove-shaped binding sites, for example, protein-protein interface because at least half of all targets assumed to be involved in human disease have been classified as “difficult to drug” with traditional small molecules. Hence, MMs such as peptides, natural products, glycans, nucleic acids with various high potent bioactivities become important targets for drug discovery programs in the recent years as they could be used for ‘undruggable” intracellular targets. Cell membrane permeability is one of the key properties of pharmacodynamically active MM drug compounds and so evaluating this property for the potential MMs is crucial. Computational prediction for cell membrane permeability of molecules is very challenging; however, recent advancement in the molecular dynamics simulations help to solve this issue partially. It is expected that MMs with high membrane permeability will enable drug discovery research to expand its borders towards intracellular targets. Further to understand the chemistry behind the permeability of MMs, it is necessary to investigate their conformational changes during the permeation through membrane and for that their interactions with the membrane field should be studied reliably because these interactions involve various non-bonding interactions such as hydrogen bonding, -stacking, charge-transfer, polarization dispersion, and non-classical weak hydrogen bonding. Therefore, parameters-based classical mechanics calculations are hardly sufficient to investigate these interactions rather, quantum mechanical (QM) calculations are essential. Fragment molecular orbital (FMO) method could be used for such purpose as it performs ab initio QM calculations by dividing the system into fragments. The present work is aimed to study the cell permeability of middle molecules using molecular dynamics simulations and FMO-QM calculations. For this purpose, a natural compound syringolin and its analogues were considered in this study. Molecular simulations were performed using NAMD and Gromacs programs with CHARMM force field. FMO calculations were performed using the PAICS program at the correlated Resolution-of-Identity second-order Moller Plesset (RI-MP2) level with the cc-pVDZ basis set. The simulations clearly show that while syringolin could not permeate the membrane, its selected analogues go through the medium in nano second scale. These correlates well with the existing experimental evidences that these syringolin analogues are membrane-permeable compounds. Further analyses indicate that intramolecular -stacking interactions in the syringolin analogues influenced their permeability positively. These intramolecular interactions reduce the polarity of these analogues so that they could permeate the lipophilic cell membrane. Conclusively, the cell membrane permeability of various middle molecules with potent bioactivities is efficiently studied using molecular dynamics simulations. Insight of this behavior is thoroughly investigated using FMO-QM calculations. Results obtained in the present study indicate that non-bonding intramolecular interactions such as hydrogen-bonding and -stacking along with the conformational flexibility of MMs are essential for amicable membrane permeation. These results are interesting and are nice example for this theoretical calculation approach that could be used to study the permeability of other middle molecules. This work was supported by Japan Agency for Medical Research and Development (AMED) under Grant Number 18ae0101047.

Keywords: fragment molecular orbital theory, membrane permeability, middle molecules, molecular dynamics simulation

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