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Article ; Online: N

Saikia, Rakhee / Das, Sanghamitra / Almin, Arzu / Mahanta, Abhijit / Sarma, Bipul / Thakur, Ashim J / Bora, Utpal

2023 Volume 21, Issue 15, Page(s) 3143–3155

Abstract: ... ...

Abstract	N
Language	English
Publishing date	2023-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d3ob00176h
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Article ; Online: The Therapeutic Potential of 4-Methoxy-1-methyl-2-oxopyridine-3-carbamide (MMOXC) Derived from Ricinine on Macrophage Cell Lines Infected with Methicillin-Resistant Strains of Staphylococcus aureus.

Suthi, Subbarayudu / Gopi, Deepika / Chaudhary, Abhijit / Sarma, Potukuchi Venkata Gurunadha Krishna

Applied biochemistry and biotechnology

2022 Volume 195, Issue 5, Page(s) 2843–2862

Abstract: The incidences of methicillin-resistant strains of Staphylococcus aureus (MRSA) and their survival inside the macrophages are the major attributes of the relapsed infections after antimicrobial therapy, and it is a global problem. In this context, we ... ...

Abstract	The incidences of methicillin-resistant strains of Staphylococcus aureus (MRSA) and their survival inside the macrophages are the major attributes of the relapsed infections after antimicrobial therapy, and it is a global problem. In this context, we have previously demonstrated 4-methoxy-1-methyl-2-oxopyridine-3-carbamide (MMOXC), a Ricinine derivative exhibiting anti-S. aureus and anti-biofilm characteristics by competitively inhibiting uridine monophosphate kinase (UMPK), UDP-N-acetyl muramyl pentapeptide ligase (Mur-F), and peptidyl deformylase, (PDF). In the present study, the stability of this competitive inhibitor MMOXC was evaluated by showing its ability to remain bound to the active sites of UMPK, Mur-F, and PDF even after increasing the incubation time, temperature, pH, and substrate concentration. On growing MRSA in fewer concentrations of MMOXC, these strains could not attain resistance to MMOXC and at the same time distinct reductions in the expression of UMPK, Mur-F, and PDF genes were noted. In vitro, infective models were generated by infecting MRSA to RAW 264.7 and human monocyte-derived macrophage (hMDM) cell lines. In these infected cell lines, in spite of increased nitric oxide synthase (NOS), NADPH-P450 reductase, superoxide dismutase, catalase, and peroxidase activities, the MRSA survived. At 640 µM/ml, the concentration of MMOXC penetrated into these infected cells and obliterated MRSA. While treating uninfected macrophage cell lines with MMOXC, no appreciable effect was observed indicating that MMOXC is the most suitable drug for the treatment of infections caused by MRSA.
MeSH term(s)	Humans ; Staphylococcus aureus ; Methicillin Resistance ; Urea/pharmacology ; Anti-Bacterial Agents/pharmacology ; Methicillin-Resistant Staphylococcus aureus ; Staphylococcal Infections/drug therapy ; Cell Line ; Microbial Sensitivity Tests
Chemical Substances	ricinine (130UFS7AE0) ; Urea (8W8T17847W) ; Anti-Bacterial Agents
Language	English
Publishing date	2022-11-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	392344-7
ISSN	1559-0291 ; 0273-2289
ISSN (online)	1559-0291
ISSN	0273-2289
DOI	10.1007/s12010-022-04269-w
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Article ; Online: Dibenzyl (benzo [d] thiazol-2-yl (hydroxy) methyl) phosphonate (DBTMP) showing anti-S. aureus and anti-biofilm properties by elevating activities of serine protease (SspA) and cysteine protease staphopain B (SspB).

Deepika, G / Subbarayadu, S / Chaudhary, Abhijit / Sarma, P V G K

Archives of microbiology

2022 Volume 204, Issue 7, Page(s) 397

Abstract: Staphylococcus aureus biofilms are the pathogenic factor in the spread of infection and are more pronounced in multidrug-resistant strains of S. aureus, where high expression of proteases is observed. Among various proteases, Serine protease (SspA) and ... ...

Abstract	Staphylococcus aureus biofilms are the pathogenic factor in the spread of infection and are more pronounced in multidrug-resistant strains of S. aureus, where high expression of proteases is observed. Among various proteases, Serine protease (SspA) and cysteine protease Staphopain B (SspB) are known to play a key role in the biofilm formation and removal of biofilms. In earlier studies, we have reported Dibenzyl (benzo [d] thiazol-2-yl (hydroxy) methyl) phosphonate (DBTMP) exhibits anti-S. aureus and anti-biofilm properties by elevating the expression of the protease. In this study, the effect of DBTMP on the activities of SspA, and SspB of S. aureus was evaluated. The SspA and SspB genes of S. aureus ATCC12600 were sequenced (Genbank accession numbers: MZ456982 and MW574006). In S. aureus active SspA is formed by proteolytic cleavage of immature SspA, to get this mature SspA (mSspA), we have PCR amplified the mSspA sequence from the SspA gene. The mSspA and SspB genes were cloned, expressed, and characterized. The pure recombinant proteins rSspB and rmSspA exhibited a single band in SDS-PAGE with a molecular weight of 40 and 30 KD, respectively. The activities of rmSspA and rSspB are 32.33 and 35.45 Units/mL correspondingly. DBTMP elevated the activities of rmSspA and rSspB by docking with respective enzymes. This compound disrupted the biofilms formed by the multidrug-resistant strains of S. aureus and further prevented biofilm formation. These findings explain that DBTMP possesses anti-S. aureus and anti-biofilm features.
MeSH term(s)	Biofilms ; Cysteine ; Cysteine Proteases/genetics ; Cysteine Proteases/metabolism ; Organophosphonates/pharmacology ; Serine Endopeptidases/genetics ; Serine Endopeptidases/metabolism ; Serine Proteases/genetics ; Staphylococcus aureus/genetics ; Staphylococcus aureus/metabolism
Chemical Substances	Organophosphonates ; Cysteine Proteases (EC 3.4.-) ; Serine Proteases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2022-06-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-022-02974-y
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Article ; Online: Physiological Temperature and Osmotic Changes Drive Dynamic Proteome Alterations in the Leptospiral Outer Membrane and Enhance Protein Export Systems.

Phukan, Homen / Sarma, Abhijit / Rex, Devasahayam Arokia Balaya / Christie, Swamidurai Arul Diana / Sabu, Sarath Kizhakkemuriyil / Hariharan, Suneetha / Prasad, Thottethodi Subrahmanya Keshava / Madanan, Madathiparambil Gopalakrishnan

Journal of proteome research

2023 Volume 22, Issue 11, Page(s) 3447–3463

Abstract: Leptospirosis, a remerging zoonosis, has no effective vaccine or an unambiguous early diagnostic reagent. Proteins differentially expressed (DE) under pathogenic conditions will be useful candidates for antileptospiral measures. We employed a ... ...

Abstract	Leptospirosis, a remerging zoonosis, has no effective vaccine or an unambiguous early diagnostic reagent. Proteins differentially expressed (DE) under pathogenic conditions will be useful candidates for antileptospiral measures. We employed a multipronged approach comprising high-resolution TMT-labeled LC-MS/MS-based proteome analysis coupled with bioinformatics on leptospiral proteins following Triton X-114 subcellular fractionation of leptospires treated under physiological temperature and osmolarity that mimic infection. Although there were significant changes in the DE proteins at the level of the entire cell, there were notable changes in proteins at the subcellular level, particularly on the outer membrane (OM), that show the significance of subcellular proteome analysis. The detergent-enriched proteins, representing outer membrane proteins (OMPs), exhibited a dynamic nature and upregulation under various physiological conditions. It was found that pathogenic proteins showed a higher proportion of upregulation compared to the nonpathogenic proteins in the OM. Further analysis identified 17 virulent proteins exclusively upregulated in the outer membrane during infection that could be useful for vaccine and diagnostic targets. The DE proteins may aid in metabolic adaptation and are enriched in pathways related to signal transduction and antibiotic biosynthesis. Many upregulated proteins belong to protein export systems such as SEC translocase, T2SSs, and T1SSs, indicating their sequential participation in protein transport to the outer leaflet of the OM. Further studies on OM-localized proteins may shed light on the pathogenesis of leptospirosis and serve as the basis for effective countermeasures.
MeSH term(s)	Humans ; Proteome/genetics ; Proteome/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Temperature ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Leptospira/metabolism ; Leptospirosis ; Vaccines
Chemical Substances	Proteome ; Bacterial Outer Membrane Proteins ; Vaccines
Language	English
Publishing date	2023-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00295
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Article ; Online: Leptospiral cell wall hydrolase (LIC_10271) binding peptidoglycan, lipopolysaccharide, and laminin and the protein show LysM and M23 domains are co-existing in pathogenic species.

Sarma, Abhijit / Dhandapani, Gunasekaran / Phukan, Homen / Bhunia, Prasun Kumar / De, Arun Kumar / Bhattacharya, Debasis / Jebasingh, T / Madanan, Madathiparambil G

Research in microbiology

2023 Volume 174, Issue 8, Page(s) 104107

Abstract: Leptospirosis, a global reemerging zoonosis caused by the spirochete Leptospira, has severe human and veterinary implications. Cell wall hydrolase (LIC_10271) with LytM (peptidase M23) and LysM domains are found to be associated with various pathogenic ... ...

Abstract	Leptospirosis, a global reemerging zoonosis caused by the spirochete Leptospira, has severe human and veterinary implications. Cell wall hydrolase (LIC_10271) with LytM (peptidase M23) and LysM domains are found to be associated with various pathogenic bacteria. These domains regulate effects on extracellular matrix and biofilm components, which promote cell wall remodeling and pathogen dissemination in the host. In this study, we present the cloning, expression, purification, and characterization of LIC_10271. To determine the localization of LIC_10271 within the inner membrane of Leptospira, Triton X-114 subcellular fractionation and immunoblot studies were performed. Furthermore, r-LIC_10271 binds with peptidoglycan, lipopolysaccharide, and laminin in a dose-dependent manner. Analysis of the signal peptide, M23, and LysM domains revealed conservation primarily within the P1 group of Leptospira, which encompasses the most pathogenic species. Moreover, the presence of native-LIC_10271 in the inner membrane and the distribution of M23 and LysM domains across pathogenic strains indicates their potential involvement in the interaction between the host and Leptospira.
MeSH term(s)	Humans ; Laminin/metabolism ; Lipopolysaccharides/metabolism ; Peptidoglycan/metabolism ; Leptospira interrogans/genetics ; Leptospira interrogans/metabolism ; Hydrolases/metabolism ; Leptospira/genetics ; Cell Wall/metabolism ; Protein Binding
Chemical Substances	Laminin ; Lipopolysaccharides ; Peptidoglycan ; Hydrolases (EC 3.-)
Language	English
Publishing date	2023-07-28
Publishing country	France
Document type	Journal Article
ZDB-ID	1004220-9
ISSN	1769-7123 ; 0923-2508
ISSN (online)	1769-7123
ISSN	0923-2508
DOI	10.1016/j.resmic.2023.104107
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Article ; Online: Leptospira

Rex, Devasahayam Arokia Balaya / Chanderasekaran, Jaikanth / Rai, Akhila Balakrishna / Phukan, Homen / Sarma, Abhijit / Prasad, Thottethodi Subrahmanya Keshava / Madanan, Madathiparambil Gopalakrishnan

Omics : a journal of integrative biology

2022 Volume 26, Issue 5, Page(s) 280–289

Abstract: Leptospirosis is one of the most important zoonotic diseases for planetary health. It is caused ... ...

Abstract	Leptospirosis is one of the most important zoonotic diseases for planetary health. It is caused by
MeSH term(s)	Host-Pathogen Interactions ; Humans ; Leptospira/metabolism ; Leptospirosis/microbiology ; Molecular Docking Simulation ; Peptides ; Protein Processing, Post-Translational ; Proteome/metabolism
Chemical Substances	Peptides ; Proteome
Language	English
Publishing date	2022-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2030312-9
ISSN	1557-8100 ; 1536-2310
ISSN (online)	1557-8100
ISSN	1536-2310
DOI	10.1089/omi.2022.0007
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Article ; Online: Molecular diversity of Mycobacterium tuberculosis isolates in Treatment-experienced Patients from Andhra Pradesh, India.

Srikar, Anagoni / Venkataramana, Banda / Mohan, Alladi / Sarma, Pvgk / Rekha Devi, Kangjam / Narain, Kanwar / Chaudhury, Abhijit

Journal of infection in developing countries

2023 Volume 17, Issue 8, Page(s) 1114–1124

Abstract: Introduction: To get a comprehensive idea about the transmission and epidemiology of TB globally and locally, the use of molecular typing methods has become imperative not only for understanding genetic diversity but also the population structure of ... ...

Abstract	Introduction: To get a comprehensive idea about the transmission and epidemiology of TB globally and locally, the use of molecular typing methods has become imperative not only for understanding genetic diversity but also the population structure of Mycobacterium tuberculosis complex (MTBC). We aimed to investigate the drug resistance pattern and genetic diversity of MTBC among previously treated patients with sputum smear-positive pulmonary tuberculosis in a South Indian population. Methodology: 104 patients with sputum smear positivity and who had previously undergone treatment were selected. Drug susceptibility testing, Spoligotyping, MIRU-VNTR, and SNP typing were performed. Results: Mono-resistance to isoniazid 16 (15.38%) was the highest among all drugs. Out of 104 isolates, 24 (23%) isolates were classified as MDR strains. The distributions of most common lineages were: EAI3-Ind-20 (19.23%), EAI5-13 (12.50%), Beijing-12 (11.54%), CAS1-Delhi- 9 (8.65%), and 7 (6.73%) each of T-H37rv, Unknown and Orphan types. MIRU-VNTR-based analysis revealed that there are two major groups: CAS1-Delhi and Beijing groups. Out of 104 isolates, 82 belonged to well-defined lineages and 6 clusters, and the remaining 22 were singletons. SNP analysis showed no mutations associated with five sets of genes in 33 strains. Conclusions: The occurrence of 11.54% Beijing strains in South India is an important finding. High frequency of Isoniazid mono resistance noticed. Spoligotyping along with MIRU-VNTR and SNP typing is the best approach to the identification of strain lineages. No mutation with Antigen85C gene represents, can be used for vaccine candidates.
MeSH term(s)	Humans ; Mycobacterium tuberculosis/genetics ; Isoniazid/pharmacology ; Isoniazid/therapeutic use ; Microbial Sensitivity Tests ; Tuberculosis, Pulmonary/drug therapy ; Tuberculosis, Pulmonary/epidemiology ; India/epidemiology
Chemical Substances	Isoniazid (V83O1VOZ8L)
Language	English
Publishing date	2023-08-31
Publishing country	Italy
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2394024-4
ISSN	1972-2680 ; 2036-6590
ISSN (online)	1972-2680
ISSN	2036-6590
DOI	10.3855/jidc.17757
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Article ; Online: Unique Posttranslational Modification Sites of Acetylation, Citrullination, Glutarylation, and Phosphorylation Are Found to Be Specific to the Proteins Partitioned in the Triton X-114 Fractions of

Phukan, Homen / Sarma, Abhijit / Rex, Devasahayam Arokia Balaya / Rai, Akhila Balakrishna / Prasad, Thottethodi Subrahmanya Keshava / Madanan, Madathiparambil Gopalakrishnan

ACS omega

2022 Volume 7, Issue 22, Page(s) 18569–18576

Abstract: Posttranslational modifications (PTMs) are decisive factors in the structure, function, and localization of proteins in prokaryotic and eukaryotic organisms. However, prokaryotic organisms lack subcellular organelles, and protein localization based on ... ...

Abstract	Posttranslational modifications (PTMs) are decisive factors in the structure, function, and localization of proteins in prokaryotic and eukaryotic organisms. However, prokaryotic organisms lack subcellular organelles, and protein localization based on subcellular locations like cytoplasm, inner membrane, periplasm, and outer membrane can be accounted for functional characterization. We have identified 131 acetylated, 1182 citrullinated, 72 glutarylated, 5 palmitoylated, and 139 phosphorylated proteins from Triton X-114 fractionated proteins of
Language	English
Publishing date	2022-05-25
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c01245
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Article ; Online: Diurnal and seasonal variability of CO

Metya, Abirlal / Datye, Amey / Chakraborty, Supriyo / Tiwari, Yogesh K / Sarma, Dipankar / Bora, Abhijit / Gogoi, Nirmali

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2931

Abstract: Amongst all the anthropogenically produced greenhouse gases (GHGs), carbon dioxide ( ... ...

Abstract	Amongst all the anthropogenically produced greenhouse gases (GHGs), carbon dioxide (CO
Language	English
Publishing date	2021-02-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-82321-1
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Article: Dibenzyl (benzo [d] thiazol-2-yl (hydroxy) methyl) phosphonate (DBTMP) showing anti-S. aureus and anti-biofilm properties by elevating activities of serine protease (SspA) and cysteine protease staphopain B (SspB)

Deepika, G. / Subbarayadu, S. / Chaudhary, Abhijit / Sarma, P. V. G. K.

Archives of microbiology. 2022 July, v. 204, no. 7

2022

Abstract	Staphylococcus aureus biofilms are the pathogenic factor in the spread of infection and are more pronounced in multidrug-resistant strains of S. aureus, where high expression of proteases is observed. Among various proteases, Serine protease (SspA) and cysteine protease Staphopain B (SspB) are known to play a key role in the biofilm formation and removal of biofilms. In earlier studies, we have reported Dibenzyl (benzo [d] thiazol-2-yl (hydroxy) methyl) phosphonate (DBTMP) exhibits anti-S. aureus and anti-biofilm properties by elevating the expression of the protease. In this study, the effect of DBTMP on the activities of SspA, and SspB of S. aureus was evaluated. The SspA and SspB genes of S. aureus ATCC12600 were sequenced (Genbank accession numbers: MZ456982 and MW574006). In S. aureus active SspA is formed by proteolytic cleavage of immature SspA, to get this mature SspA (mSspA), we have PCR amplified the mSspA sequence from the SspA gene. The mSspA and SspB genes were cloned, expressed, and characterized. The pure recombinant proteins rSspB and rmSspA exhibited a single band in SDS–PAGE with a molecular weight of 40 and 30 KD, respectively. The activities of rmSspA and rSspB are 32.33 and 35.45 Units/mL correspondingly. DBTMP elevated the activities of rmSspA and rSspB by docking with respective enzymes. This compound disrupted the biofilms formed by the multidrug-resistant strains of S. aureus and further prevented biofilm formation. These findings explain that DBTMP possesses anti-S. aureus and anti-biofilm features.
Keywords	biofilm ; cysteine proteinases ; genes ; microbiology ; molecular weight ; multiple drug resistance ; phosphonates ; polyacrylamide gel electrophoresis ; proteolysis ; serine proteinases
Language	English
Dates of publication	2022-07
Size	p. 397.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-022-02974-y
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