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  1. Article ; Online: Molecular characterization of biosurfactant producing marine bacterium isolated from hydrocarbon-contaminated soil using 16S rRNA gene sequencing

    Sethuramalingam Balakrishnan / Narasingam Arunagirinathan / Marimuthu Ragavan Rameshkumar / Purushothaman Indu / Nallusamy Vijaykanth / Khalid S. Almaary / Saeedah Musaed Almutairi / Tse-Wei Chen

    Journal of King Saud University: Science, Vol 34, Iss 3, Pp 101871- (2022)

    2022  

    Abstract: Objectives: This study was aimed to isolate and identify the biosurfactant producing marine bacteria from petroleum hydrocarbons contaminated sediments by 16S rRNA gene sequencing. Methods: Soil sample was enriched with diesel (2%) as the sole source of ... ...

    Abstract Objectives: This study was aimed to isolate and identify the biosurfactant producing marine bacteria from petroleum hydrocarbons contaminated sediments by 16S rRNA gene sequencing. Methods: Soil sample was enriched with diesel (2%) as the sole source of carbon in minimal salt medium for 3 weeks at 28 °C ± 2. Enriched sample was plated on nutrient agar and the organisms are selected based on the colony morphology. Biosurfactant producing efficiency of the isolates was assessed using blood haemolysis, oil displacement test, microplate assay (drop collapse test) and emulsification activity. Identification of the efficient biosurfactant producing isolate was done by gram staining and biochemical tests. Molecular characterization was done using 16S rRNA gene sequencing. Results: Totally seven isolates were selected based on colony morphology and among them, the isolate ADY2b was able to reduce surface tension significantly in the oil displacement test and also formed a stable emulsion. The emulsification index (E24) had shown a promising result of 58.33%. The isolate ADY2b was a motile, gram negative rod shaped bacterium and positive for catalase and oxidase. Sequence alignment of the 16S rRNA of the ADY2b strain and database search revealed 98% similarity to Pseudomonas mendocina by BLAST analysis. Conclusion: Seven bacteria were isolated from petroleum hydrocarbon contaminated sediments. Strain ADY2b had shown promising results on the production of biosurfactants and it is capable of increasing the bioavailability of poorly soluble petroleum hydrocarbons. The isolate Pseudomonas mendocina ADY2b obtained in the study had potential to be used in oil degradation purposes.
    Keywords Biosurfactants ; Petroleum hydrocarbons ; 16S rRNA ; Microplate assay ; Emulsification activity (E24) ; Pseudomonas species ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Computational screening of dual inhibitors from FDA approved antiviral drugs on SARS-CoV-2 spike protein and the main protease using molecular docking approach.

    Sabarimurugan, Shanthi / Purushothaman, Indu / Swaminathan, Rajarajan / Dharmarajan, Arun / Warrier, Sudha / Kothandan, Sangeetha

    Acta virologica

    2021  Volume 65, Issue 2, Page(s) 160–172

    Abstract: The deadly disease-causing novel coronavirus has recently swept across the world and endangered many human lives. Although, various research on therapeutic measures to solve this pandemic crisis has been published; no favourable results have been ... ...

    Abstract The deadly disease-causing novel coronavirus has recently swept across the world and endangered many human lives. Although, various research on therapeutic measures to solve this pandemic crisis has been published; no favourable results have been achieved. We propose the use of potential FDA-approved dual inhibitors which can inhibit two targets (either on entry-level or the main protease) for the effective treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We screened 12 FDA-approved antiviral inhibitors listed in Drug bank and analysed the ADMET properties of each drug of interest to study the bioavailability, safety and toxicity. Two potential targets, the spike protein and the main protease of SARS-CoV-2 obtained from PDB have been used for molecular docking. All the selected drugs were docked with both targets and demonstrated strong hydrogen bond (HB) interactions in multiple active sites. Amongst these, the range of binding energy was from 3-7 kcal/mol for spike protein and 2-8 kcal/mol for the main protease. Upon comparison of all the processed drugs ganciclovir and zanamivir displayed significant binding energy with HB interactions with both, spike (-9.2 and -9 kcal/mol respectively) and the main protease (-9 kcal/mol). Ribavirin and tenofovir showed significant binding energy above -8 kcal/mol with seven HB interactions with the main protease and also spike protein. The novel findings regarding the antiviral properties of these dual inhibitors using a computational approach will be a good starting point for the efficacy determination of these drugs for pre-clinical and clinical studies aimed at developing active antivirals to target SARS-CoV-2. Keywords: SARS-CoV-2; FDA-approved drugs; viral inhibitors; in-silico analysis; molecular docking.
    MeSH term(s) Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Antiviral Agents ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2021-06-15
    Publishing country Slovakia
    Document type Journal Article
    ZDB-ID 210452-0
    ISSN 1336-2305 ; 0001-723X
    ISSN (online) 1336-2305
    ISSN 0001-723X
    DOI 10.4149/av_2021_208
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Different Donor-Acceptor Interactions of Carbene Ligands in Heteroleptic Divalent Group 14 Compounds, LEL' (E=C-Sn; L=N-Heterocyclic Carbene; L'=Cyclic Alkyl(Amino) Carbene).

    Purushothaman, Indu / De, Susmita / Parameswaran, Pattiyil

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2018  Volume 24, Issue 15, Page(s) 3816–3824

    Abstract: The electronic structure and reactivity of heteroleptic divalent group 14 compounds, 1E (E=C-Sn) with NHC and cAAC ligands have been studied at the BP86/TZ2P level of theory and compared with homoleptic group 14 compounds. The EDA-NOCV (energy ... ...

    Abstract The electronic structure and reactivity of heteroleptic divalent group 14 compounds, 1E (E=C-Sn) with NHC and cAAC ligands have been studied at the BP86/TZ2P level of theory and compared with homoleptic group 14 compounds. The EDA-NOCV (energy decomposition analysis-natural orbitals for chemical valence) analysis indicates that the interaction between the two carbene ligands and the central C-atom in 1C can be best represented as one 3c-2e electron sharing σ-bond and one 3c-2e donor-acceptor σ-bond. There exists an electron sharing interaction between the π-type orbital on the central C-atom and the C-N π* orbital of cAAC and a π-back-donation from the σ-type lone pair on the central C-atom to the π*-MO of NHC. This bonding description is equivalent to the localized bonding representation, where the central C-atom forms two electron sharing bonds and two donor-acceptor bonds with cAAC and NHC ligands. However, the bonding between the carbene ligands and the heavier group 14 element can be best represented as two 2c-2e donor-acceptor σ-bonds and a π-back-donation from group 14 element to C-N π* orbital of cAAC. This bonding description is well supported by the geometrical and Natural Bond Orbital (NBO) analyses. Hence, 1C can be best described as a carbene and the heavier analogues can be best described as tetrylones. However, the high first (287.6-274.3 kcal mol
    Language English
    Publishing date 2018-03-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-x
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.201705719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins

    Marimuthu Ragavan Rameshkumar / Purushothaman Indu / Narasingam Arunagirinathan / Babu Venkatadri / Hamed A. El-Serehy / Ajaz Ahmad

    Saudi Journal of Biological Sciences, Vol 28, Iss 1, Pp 448-

    A molecular docking study

    2021  Volume 458

    Abstract: An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent ... ...

    Abstract An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent need. In this study, flavonoid compounds were analyzed for its inhibitory potential against important protein targets of SARS-CoV-2 using computational approaches. Virtual docking was performed for screening of flavonoid compounds retrieved from PubChem against the main protease of SARS-CoV-2 using COVID-19 docking server. The cut off of dock score was set to >−9 kcal/mol and screened compounds were individually docked against main protease, RNA-dependent RNA polymerase, and spike proteins using AutoDock 4.1 software. Finally, lead flavonoid compounds were subjected to ADMET analysis. A total of 458 flavonoid compounds were virtually screened against main protease target and 36 compounds were selected based on the interaction energy value >−9 kcal/mol. Furthermore, these compounds were individually docked against protein targets and top 10 lead compounds were identified. Among the lead compounds, agathisflavone showed highest binding energy value of −8.4 kcal/mol against main protease, Albireodelphin showed highest dock score of −9.8 kcal/mol and −11.2 kcal/mol against RdRp, and spike proteins, respectively. Based on the high dock score and ADMET properties, top 5 lead molecules such as Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate were identified as potent inhibitors against main protease, RdRp, and spike protein targets of SARS-CoV-2. These all compounds are having non-carcinogenic and non-mutagenic properties. This study finding suggests that the screened compounds include Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin ...
    Keywords COVID-19 ; SARS-CoV-2 ; Flavonoid compounds ; ADMET analysis ; Antiviral drug ; Main protease ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Spectral characterisation, antiviral activities, in silico ADMET and molecular docking of the compounds isolated from Tectona grandis to chikungunya virus.

    K, Sangeetha / Purushothaman, Indu / S, Rajarajan

    Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    2017  Volume 87, Page(s) 302–310

    Abstract: Chikungunya infection is treated symptomatically with antipyretics and anti-inflammatory drugs without any specific antiviral drug till date. The lack of an approved antiviral drug and the emergence of virulent strains after 2006 epidemics emphasize the ... ...

    Abstract Chikungunya infection is treated symptomatically with antipyretics and anti-inflammatory drugs without any specific antiviral drug till date. The lack of an approved antiviral drug and the emergence of virulent strains after 2006 epidemics emphasize the need for the development of potential antiviral drugs to Chikungunya virus. Hence, we studied the antiviral activity of the extracts and compounds isolated from Tectona grandis leaves to both the Asian and East central South African strains of Chikungunya virus. Five compounds were isolated from the ethanolic extract of Tectona grandis by bioactivity guided fractionation followed by Spectral Characterisation through GC-MS and NMR spectroscopy and investigated for the antiviral activity. Also in silico ADMET and Molecular Docking of the characterised compounds against the structural and non structural proteins of Chikungunya virus were performed. The characterised compound Benzene-1-carboxylic acid hexadeconate was effective at IC 50 3.036μg/ml (7.5μM) and 76.46μg/ml (189.02μM) to Asian and ECSA strain of CHIKV respectively. The compound showed desirable pharmacokinetic properties and significant molecular interactions with the E1 protein of Chikungunya virus by in silico analysis. Thus Benzene-1-carboxylic acid-2-hexadeconate isolated from Tectona grandis was found to be a promising drug candidate to both the Asian and ECSA strains of Chikungunya virus with high selectivity indices in comparison to the reference RNA antiviral drug Ribavirin.
    MeSH term(s) Animals ; Antiviral Agents/isolation & purification ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Cercopithecus aethiops ; Chikungunya virus/drug effects ; Chikungunya virus/metabolism ; Computer Simulation ; Gas Chromatography-Mass Spectrometry/methods ; Humans ; Lamiaceae ; Magnetic Resonance Spectroscopy/methods ; Molecular Docking Simulation/methods ; Plant Extracts/isolation & purification ; Plant Extracts/metabolism ; Plant Extracts/pharmacology ; Vero Cells
    Chemical Substances Antiviral Agents ; Plant Extracts
    Language English
    Publishing date 2017-03
    Publishing country France
    Document type Journal Article
    ZDB-ID 392415-4
    ISSN 1950-6007 ; 0753-3322 ; 0300-0893
    ISSN (online) 1950-6007
    ISSN 0753-3322 ; 0300-0893
    DOI 10.1016/j.biopha.2016.12.069
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2

    Purushothaman Indu / Marimuthu Ragavan Rameshkumar / Narasingam Arunagirinathan / Naif Abdullah Al-Dhabi / Mariadhas Valan Arasu / Savarimuthu Ignacimuthu

    Journal of Infection and Public Health, Vol 13, Iss 12, Pp 1856-

    A molecular docking and drug repurposing approach

    2020  Volume 1861

    Abstract: Background: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to ... ...

    Abstract Background: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to find out the drugs for COVID-19 treatment from existing FDA approved antiviral drugs. In this study, FDA approved small molecule antiviral drugs were repurposed against the major viral proteins of SARS-CoV-2. Methods: The 3D structures of FDA approved small molecule antiviral drugs were retrieved from PubChem. Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. Furthermore, lead molecules were individually docked against protein targets using AutoDock 4.0.1 software and their drug-likeness and ADMET properties were evaluated. Results: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥−8 kcal/mol. Similarly Indinavir showed the highest binding energy of -11.5 kcal/mol against the target protein RdRp and Dolutegravir, Elbasvir, Tipranavir, Taltegravir, Grazoprevir, Daclatasvir, Glecaprevir, Ledipasvir, Pibrentasvir and Velpatasvir showed a binding energy value in range from -8 to -11.2 kcal/mol. The antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine also exhibited good bioavailability and drug-likeness properties. Conclusion: This study suggests that the screened small molecule antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine could serve as potential drugs for the treatment of COVID-19 with further validation studies.
    Keywords COVID-19 ; SARS-CoV-2 ; Main protease ; RNA-dependent RNA polymerase ; Antiviral drugs ; Docking ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: CO2 adducts of Lewis acid–base pairs (LBCO2LA; LB = PMe3, NHC and LA = AlH3, AlCl3, BH3) − analogous to carboxylic acids and their derivatives

    Purushothaman, Indu / De, Susmita / Parameswaran, Pattiyil

    RSC advances. 2014 Nov. 12, v. 4, no. 104

    2014  

    Abstract: The relationship between the structure and bonding of two different classes of molecules helps to understand and correlate their physiochemical activity. Here, we report the structure-bonding analogy between CO2 adducts of a Lewis acid (LA)–Lewis base ( ... ...

    Abstract The relationship between the structure and bonding of two different classes of molecules helps to understand and correlate their physiochemical activity. Here, we report the structure-bonding analogy between CO2 adducts of a Lewis acid (LA)–Lewis base (LB) pairs, LBCO2LA (LB = PMe3 and NHC; LA = AlH3, AlCl3 and BH3) and carboxylic acids and their derivatives, RCO2R′ (R, R′ = alkyl, H) by quantum mechanical calculations. The direction of charge flow in LBCO2LA is from LB to LA, whereas the reverse direction of charge flow (R′ to R) is observed for RCO2R′ leading to a formally negatively charged CO2 group (2A1) in both systems. This negatively charged bent CO2 group plays a deterministic role towards its bonding interaction with other fragments. The bonding analysis by the EDA-NOCV method indicates that both the LB and R groups form an electron sharing bond with the carbon atom of the bent CO2 fragment, whereas both LA and R′ form a donor–acceptor interaction with the oxygen atom. Our analysis suggests that the CO2 adducts of the Lewis acid (LA)–Lewis base (LB) pairs, LBCO2LA, can be considered as inorganic analogues of carboxylic acids and their derivatives, RCO2R′.
    Keywords aluminum chloride ; boranes ; carbon ; carbon dioxide ; carboxylic acids ; Lewis acids ; oxygen ; quantum mechanics
    Language English
    Dates of publication 2014-1112
    Size p. 60421-60428.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ISSN 2046-2069
    DOI 10.1039/c4ra10269j
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Detection of blaNDM-1 and blaNDM-5 genes among Gram-negative bacteria isolated from human immunodeficiency virus patients in South India

    Marimuthu Ragavan Rameshkumar / Narasingam Arunagirinathan / Purushothaman Indu / Chinnambedu Ravichandran Swathirajan / Sunil Suhas Solomon / Ramachandran Vignesh / Pachamuthu Balakrishnan

    Journal of Research in Medical Sciences, Vol 23, Iss 1, Pp 112-

    2018  Volume 112

    Keywords Medicine ; R
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Stepwise isolation of an unprecedented silylene supported dinuclear gold(i) cation with aurophilic interaction.

    Khan, Shabana / Pal, Shiv / Kathewad, Neha / Purushothaman, Indu / De, Susmita / Parameswaran, Pattiyil

    Chemical communications (Cambridge, England)

    2016  Volume 52, Issue 20, Page(s) 3880–3882

    Abstract: The silylene (PhC(NtBu)2SiN(PPh2)(2,6-iPr2-C6H3)) (2) was prepared from the previously reported (PhC(NtBu)2SiCl) salt elimination method. The reaction of 2 with AuCl(SMe2) afforded [(PhC(NtBu)2SiN(PPh2)(2,6-iPr2-C6H3))AuCl] (3). Note here that only Si(ii) ...

    Abstract The silylene (PhC(NtBu)2SiN(PPh2)(2,6-iPr2-C6H3)) (2) was prepared from the previously reported (PhC(NtBu)2SiCl) salt elimination method. The reaction of 2 with AuCl(SMe2) afforded [(PhC(NtBu)2SiN(PPh2)(2,6-iPr2-C6H3))AuCl] (3). Note here that only Si(ii) is coordinated to Au(i), while P(iii) remains uncoordinated. The higher negative value of the electrostatic potential (ESP) at the Si-centre (-28.8 kcal mol(-1)) as compared to that at the P-centre (-15.3 kcal mol(-1)) justifies this observation. Furthermore, the chloride abstraction from 3 by AgSbF6 led to the formation of a dinuclear Au(i) cationic complex, [PhC(NtBu)2Si(2,6-iPr2-C6H3NPPh2)(Au)]2[SbF6]2 (4), which displays an intra-molecular Au...Au interaction of 2.865 Å.
    MeSH term(s) Cations/chemistry ; Gold/chemistry ; Models, Molecular ; Molecular Structure ; Organogold Compounds/chemical synthesis ; Organogold Compounds/chemistry ; Organogold Compounds/isolation & purification ; Organosilicon Compounds/chemistry
    Chemical Substances Cations ; Organogold Compounds ; Organosilicon Compounds ; Gold (7440-57-5)
    Language English
    Publishing date 2016-03-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c6cc00597g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Trapping a Silicon(I) Radical with Carbenes: A Cationic cAAC-Silicon(I) Radical and an NHC-Parent-Silyliumylidene Cation.

    Li, Yan / Chan, Yuk-Chi / Leong, Bi-Xiang / Li, Yongxin / Richards, Emma / Purushothaman, Indu / De, Susmita / Parameswaran, Pattiyil / So, Cheuk-Wai

    Angewandte Chemie (International ed. in English)

    2017  Volume 56, Issue 26, Page(s) 7573–7578

    Abstract: The trapping of a silicon(I) radical with N-heterocyclic carbenes is described. The reaction of the cyclic (alkyl)(amino) carbene [ ... ...

    Abstract The trapping of a silicon(I) radical with N-heterocyclic carbenes is described. The reaction of the cyclic (alkyl)(amino) carbene [cAAC
    Language English
    Publishing date 2017-05-24
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.201702760
    Database MEDical Literature Analysis and Retrieval System OnLINE

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