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Jiang Y, Rex DAB, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Mayta ML, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry. ArXiv 2023:arXiv:2311.07791v1. [PMID: 38013887 PMCID: PMC10680866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.
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Vanuopadath M, Rajan K, Alangode A, Nair SS, Nair BG. The Need for Next-Generation Antivenom for Snakebite Envenomation in India. Toxins (Basel) 2023; 15:510. [PMID: 37624267 PMCID: PMC10467155 DOI: 10.3390/toxins15080510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023] Open
Abstract
The limitations posed by currently available antivenoms have emphasized the need for alternative treatments to counteract snakebite envenomation. Even though exact epidemiological data are lacking, reports have indicated that most global snakebite deaths are reported in India. Among the many problems associated with snakebite envenomation, issues related to the availability of safer and more efficient antivenoms are of primary concern. Since India has the highest number of global snakebite deaths, efforts should be made to reduce the burden associated with snakebite envenoming. Alternative methods, including aptamers, camel antivenoms, phage display techniques for generating high-affinity antibodies and antibody fragments, small-molecule inhibitors, and natural products, are currently being investigated for their effectiveness. These alternative methods have shown promise in vitro, but their in vivo effectiveness should also be evaluated. In this review, the issues associated with Indian polyvalent antivenoms in neutralizing venom components from geographically distant species are discussed in detail. In a nutshell, this review gives an overview of the current drawbacks of using animal-derived antivenoms and several alternative strategies that are currently being widely explored.
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Affiliation(s)
| | | | | | | | - Bipin Gopalakrishnan Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690 525, Kerala, India; (M.V.); (K.R.); (A.A.); (S.S.N.)
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Vanuopadath M, Raveendran D, Nair BG, Nair SS. Venomics and antivenomics of Indian spectacled cobra (Naja naja) from the Western Ghats. Acta Trop 2022; 228:106324. [PMID: 35093326 DOI: 10.1016/j.actatropica.2022.106324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/03/2023]
Abstract
Venom proteome profiling of Naja naja from the Western Ghats region in Kerala was achieved through SDS-PAGE and RP-HPLC followed by Q-TOF LC-MS/MS analysis, incorporating PEAKS and Novor assisted de novo sequencing methodologies. A total of 115 proteins distributed across 17 different enzymatic and non-enzymatic venom protein families were identified through conventional and 39 peptides through homology-driven proteomics approaches. Fourteen peptides derived through de novo complements the Mascot data indicating the importance of homology-driven approaches in improving protein sequence information. Among the protein families identified, glutathione peroxidase and endonuclease were reported for the first time in the Indian cobra venom. Immunological cross-reactivity assessed using Indian polyvalent antivenoms suggested that VINS showed better EC50 (2.48 µg/mL) value than that of PSAV (6.04 µg/mL) and Virchow (6.03 µg/mL) antivenoms. Western blotting experiments indicated that all the antivenoms elicited poor binding specificities, especially towards low molecular mass proteins. Second-generation antivenomics studies revealed that VINS antivenom was less efficient to detect many low molecular mass proteins such as three-finger toxins and Kunitz-type serine protease Inhibitors. Taken together, the present study enabled a large-scale characterization of the venom proteome of Naja naja from the Western Ghats and emphasized the need for developing more efficient antivenoms.
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Affiliation(s)
| | - Dileepkumar Raveendran
- Indriyam Biologics Pvt. Ltd., SCTIMST-TIMed, BMT Wing-Poojappura, Thiruvananthapuram 695 012, Kerala, India
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Chouhan S, Singh S, Athavale D, Ramteke P, Vanuopadath M, Nair BG, Nair SS, Bhat MK. Sensitization of hepatocellular carcinoma cells towards doxorubicin and sorafenib is facilitated by glucose-dependent alterations in reactive oxygen species, P-glycoprotein and DKK4. J Biosci 2020. [DOI: 10.1007/s12038-020-00065-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Drishya G, Nambiar J, Shaji SK, Vanuopadath M, Achuthan A, Kumar A, Alias A, Sherif A, Joseph C, Divya P, Kumar DS, Bose C, Nair SV, Sudarslal S, Kumar GB, Lakshmi S, Nair BG. RECK and TIMP-2 mediate inhibition of MMP-2 and MMP-9 by Annona muricata. J Biosci 2020. [DOI: 10.1007/s12038-020-00056-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Vanuopadath M, Shaji SK, Raveendran D, Nair BG, Nair SS. Delineating the venom toxin arsenal of Malabar pit viper (Trimeresurus malabaricus) from the Western Ghats of India and evaluating its immunological cross-reactivity and in vitro cytotoxicity. Int J Biol Macromol 2020; 148:1029-1045. [PMID: 31982532 DOI: 10.1016/j.ijbiomac.2020.01.226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
The venom protein components of Malabar pit viper (Trimeresurus malabaricus) were identified by combining SDS-PAGE and ion-exchange chromatography pre-fractionation techniques with LC-MS/MS incorporating Novor and PEAKS-assisted de novo sequencing strategies. Total 97 proteins that belong to 16 protein families such as L-amino acid oxidase, metalloprotease, serine protease, phospholipase A2, 5'-nucleotidase, C-type lectins/snaclecs and disintegrin were recognized from the venom of a single exemplar species. Of the 97 proteins, eighteen were identified through de novo approaches. Immunological cross-reactivity assessed through ELISA and western blot indicate that the Indian antivenoms binds less effectively to Malabar pit viper venom components compared to that of Russell's viper venom. The in vitro cell viability assays suggest that compared to the normal cells, MPV venom induces concentration dependent cell death in various cancer cells. Moreover, crude venom resulted in chromatin condensation and apoptotic bodies implying the induction of apoptosis. Taken together, the present study enabled in dissecting the venom proteome of Trimeresurus malabaricus and revealed the immuno-cross-reactivity profiles of commercially available Indian polyvalent antivenoms that, in turn, is expected to provide valuable insights on the need in improving antivenom preparations against its bite.
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Affiliation(s)
| | | | - Dileepkumar Raveendran
- Indriyam Biologics Pvt. Ltd., SCTIMST-TIMed, BMT Wing-Poojappura, Thiruvananthapuram 695 012, Kerala, India
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Drishya G, Nambiar J, Shaji SK, Vanuopadath M, Achuthan A, Kumar A, Alias A, Sherif A, Joseph C, Divya P, Kumar DS, Bose C, Nair SV, Sudarslal S, Kumar GB, Lakshmi S, Nair BG. RECK and TIMP-2 mediate inhibition of MMP-2 and MMP-9 by Annona muricata. J Biosci 2020; 45:89. [PMID: 32661216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Up-regulation of MMP-2 and MMP-9 plays a significant role in promoting cancer progression by degrading the components of the extracellular matrix, thereby enhancing the migration of tumor cells. Although the antiproliferative and apoptotic effect of Annona muricata is well established, its effect on MMP-2 and MMP-9, a major target in several types of cancers, has not been studied. Powdered samples of various parts of A. muricata like fruit, stem, seed, and twig extracted using aqueous methanol showed significant dose-dependent inhibition of MMP-2 and MMP-9 in a highly metastatic fibrosarcoma cell line, HT1080. Additionally, these extracts also up-regulated the expression of several endogenous inhibitors of MMP-2 and MMP-9 like REversion-inducing Cysteine-rich protein with Kazal motifs (RECK) and Tissue Inhibitor of Metalloproteinase- 2 (TIMP-2). Furthermore, primary cells developed from tumor tissues obtained from patients not exposed to chemotherapy, also exhibited similar results. Remarkably, the inhibition of MMP-2 and MMP-9 observed was tumor specific, with the A. muricata fruit extract showing only 2% inhibition in cells obtained from normal tissues, when compared to 60% inhibition observed in cells obtained from tumor samples. The present study elucidates a novel mechanism by which A. muricata extracts selectively exhibit their anti-cancer activity in tumor cells by down-regulating MMP-2 and MMP-9 that are important biomarkers in cancer.
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Affiliation(s)
- G Drishya
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam 690 525, India
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Chouhan S, Singh S, Athavale D, Ramteke P, Vanuopadath M, Nair BG, Nair SS, Bhat MK. Sensitization of hepatocellular carcinoma cells towards doxorubicin and sorafenib is facilitated by glucosedependent alterations in reactive oxygen species, P-glycoprotein and DKK4. J Biosci 2020; 45:97. [PMID: 32713860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Altered glucose uptake and metabolism is the key characteristic of cancer cells including hepatocellular carcinoma (HCC). However, role of glucose availability in chemotherapeutic outcome of HCC is unclear. The present study investigates the effect of glucose facilitated sensitization of HCC cells towards doxorubicin (DOX) and sorafenib (SORA). In HCC cells, we observed that hyperglycemic culture condition (HG) is associated with increased sensitivity towards DOX and SORA. P-glycoprotein (P-gp), a transporter involved in drug efflux, was elevated in HCC cells in NG, rendering them less susceptible to DOX and SORA. Further, this study demonstrated that knockdown of dickkopf protein 4 (DKK4), a Wnt antagonist protein, causes enhanced glucose uptake and reduction in P-gp level rendering HCC cells in NG sensitive to DOX and SORA. Moreover, HG elevates the level of intracellular reactive oxygen species (ROS), which regulates P-gp. Alteration in intracellular ROS did not directly affect regulation of DKK4 in HCC cells. Functional assays suggest that alterations in DKK4 and P-gp level in HCC cells are dependent on glucose availability and changes in ROS level because of enhanced glucose utilization, respectively. Collectively, the present study highlights direct involvement of glucose-induced ROS, DKK4 and P-gp in altering the sensitivity of HCC cells towards DOX and SORA.
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Affiliation(s)
- Surbhi Chouhan
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune 411 007, India
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Nedungadi D, Binoy A, Vinod V, Vanuopadath M, Nair SS, Nair BG, Mishra N. Ginger extract activates caspase independent paraptosis in cancer cells via ER stress, mitochondrial dysfunction, AIF translocation and DNA damage. Nutr Cancer 2019; 73:147-159. [PMID: 31690139 DOI: 10.1080/01635581.2019.1685113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 01/01/2023]
Abstract
The rhizome of ginger (Zingiber officinale) a common culinary agent is also known for its medicinal activity. We have earlier reported that pure 6-shogaol, an important component of ginger induces paraptosis in triple negative breast cancer (MDA-MB-231) and non small cell lung (A549) cancer cells. However, the chemopreventive potential of the whole ginger extract in food remains to be elucidated. Here, we demonstrate for the first time that ginger extract (GE) triggers similar anticancer activity/paraptosis against the same cell lines but through different molecular mechanisms. Q-TOF LC-MS analysis of the extract showed the presence of several other metabolites along with 6-shogaol and 6-gingerol. GE induces cytoplasmic vacuolation through ER stress and dilation of the ER. Drastic decrease in the mitochondrial membrane potential and ATP production along with the excess generation of ROS contributed to mitochondrial dysfunction. Consequently, GE caused the translocation of apoptosis inducing factor to the nucleus leading to the fragmentation of DNA. Taken together, these show a novel mechanism for ginger extract induced cancer cell death that can be of potential interest for cancer preventive strategies.
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Affiliation(s)
- Divya Nedungadi
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Anupama Binoy
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Vivek Vinod
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, India
| | | | | | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Nandita Mishra
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
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Pushkaran AC, Vinod V, Vanuopadath M, Nair SS, Nair SV, Vasudevan AK, Biswas R, Mohan CG. Combination of Repurposed Drug Diosmin with Amoxicillin-Clavulanic acid Causes Synergistic Inhibition of Mycobacterial Growth. Sci Rep 2019; 9:6800. [PMID: 31043655 PMCID: PMC6494880 DOI: 10.1038/s41598-019-43201-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Effective therapeutic regimens for the treatment of tuberculosis (TB) are limited. They are comprised of multiple drugs that inhibit the essential cellular pathways in Mycobacterium tuberculosis (Mtb). The present study investigates an approach which enables a combination of Amoxicillin-Clavulanic acid (AMC) and a repurposed drug for its synergistic effect towards TB treatment. We identified Diosmin (DIO), by targeting the active site residues of L,D-transpeptidase (Ldt) enzymes involved in Mtb cell wall biosynthesis by using a structure-based drug design method. DIO is rapidly converted into aglycone form Diosmetin (DMT) after oral administration. Binding of DIO or DMT towards Ldt enzymes was studied using molecular docking and bioassay techniques. Combination of DIO (or DMT) and AMC exhibited higher mycobactericidal activity against Mycobacterium marinum as compared to individual drugs. Scanning electron microscopy study of M. marinum treated with AMC-DIO and AMC-DMT showed marked cellular leakage. M. marinum infected Drosophila melanogaster fly model showed an increased fly survival of ~60% upon treatment with a combination of AMC and DIO (or DMT). Finally, the enhanced in vitro antimicrobial activity of AMC-DIO was validated against Mtb H37Ra and a MDR clinical isolate. Our results demonstrate the potential for AMC and DIO (or DMT) as a synergistic combination for the treatment of TB.
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Affiliation(s)
- Anju Choorakottayil Pushkaran
- Center for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, 682 041, Kerala, India
| | - Vivek Vinod
- Center for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, 682 041, Kerala, India
| | | | | | - Shantikumar V Nair
- Center for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, 682 041, Kerala, India
| | - Anil Kumar Vasudevan
- Department of Microbiology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, 682 041, Kerala, India
| | - Raja Biswas
- Center for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, 682 041, Kerala, India.
| | - Chethampadi Gopi Mohan
- Center for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, 682 041, Kerala, India.
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Vanuopadath M, Sajeev N, Murali AR, Sudish N, Kangosseri N, Sebastian IR, Jain ND, Pal A, Raveendran D, Nair BG, Nair SS. Mass spectrometry-assisted venom profiling of Hypnale hypnale found in the Western Ghats of India incorporating de novo sequencing approaches. Int J Biol Macromol 2018; 118:1736-1746. [DOI: 10.1016/j.ijbiomac.2018.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/23/2018] [Accepted: 07/05/2018] [Indexed: 11/29/2022]
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Haripriyan J, Omanakuttan A, Menon ND, Vanuopadath M, Nair SS, Corriden R, Nair BG, Nizet V, Kumar GB. Clove Bud Oil Modulates Pathogenicity Phenotypes of the Opportunistic Human Pathogen Pseudomonas aeruginosa. Sci Rep 2018; 8:3437. [PMID: 29467483 PMCID: PMC5821892 DOI: 10.1038/s41598-018-19771-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/08/2018] [Indexed: 02/01/2023] Open
Abstract
Earlier studies from our laboratory have demonstrated that clove bud oil (CBO) attenuates expression of certain virulence factors of Pseudomonas aeruginosa PAO1. Here, we probe more deeply into the effect of CBO on four pseudomonal proteases - elastase A, elastase B, protease IV and alkaline protease - each known to play key roles in disease pathogenesis. CBO inhibited the activity of these proteases present in the bacterial culture supernatant. Zymography studies indicated that these proteases can activate host matrix metalloproteases (MMPs) to establish infection, through conversion of pro-MMP-2 to active MMP-2. PAO1 is a predominant pathogen in burn wound infections and we show the modulatory effect of CBO on MMPs in an in vitro model of burn injury. Furthermore, CBO induced dose-dependent neutrophil extracellular trap formation in human neutrophils. CBO also increased the survival of C. elegans infected with PAO1, establishing an anti-infective role in a whole animal model of pathogenesis. LC-MS/MS analysis indicated that CBO treatment elicited a significant reduction of signalling molecules (Acyl-Homoserine-Lactone) involved in quorum sensing regulation. Our observations demonstrate that CBO attenuates key virulence mechanisms of this important human pathogen, while concomitantly enhancing host innate immunomodulatory functions, with potential implications for topical therapy against antibiotic-resistant infections.
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Affiliation(s)
- Jayalekshmi Haripriyan
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Athira Omanakuttan
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Nitasha D Menon
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Muralidharan Vanuopadath
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Sudarslal Sadasivan Nair
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Ross Corriden
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Bipin G Nair
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 920093, USA
| | - Geetha B Kumar
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India.
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Chatterjee M, D'Morris S, Paul V, Warrier S, Vasudevan AK, Vanuopadath M, Nair SS, Paul-Prasanth B, Mohan CG, Biswas R. Mechanistic understanding of Phenyllactic acid mediated inhibition of quorum sensing and biofilm development in Pseudomonas aeruginosa. Appl Microbiol Biotechnol 2017; 101:8223-8236. [PMID: 28983655 DOI: 10.1007/s00253-017-8546-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa depends on its quorum sensing (QS) system for its virulence factors' production and biofilm formation. Biofilms of P. aeruginosa on the surface of indwelling catheters are often resistant to antibiotic therapy. Alternative approaches that employ QS inhibitors alone or in combination with antibiotics are being developed to tackle P. aeruginosa infections. Here, we have studied the mechanism of action of 3-Phenyllactic acid (PLA), a QS inhibitory compound produced by Lactobacillus species, against P. aeruginosa PAO1. Our study revealed that PLA inhibited the expression of virulence factors such as pyocyanin, protease, and rhamnolipids that are involved in the biofilm formation of P. aeruginosa PAO1. Swarming motility, another important criterion for biofilm formation of P. aeruginosa PAO1, was also inhibited by PLA. Gene expression, mass spectrometric, functional complementation assays, and in silico data indicated that the quorum quenching and biofilm inhibitory activities of PLA are attributed to its ability to interact with P. aeruginosa QS receptors. PLA antagonistically binds to QS receptors RhlR and PqsR with a higher affinity than its cognate ligands N-butyryl-L-homoserine lactone (C4-HSL) and 2-heptyl-3,4-dihydroxyquinoline (PQS; Pseudomonas quinolone signal). Using an in vivo intraperitoneal catheter-associated medaka fish infection model, we proved that PLA inhibited the initial attachment of P. aeruginosa PAO1 on implanted catheter tubes. Our in vitro and in vivo results revealed the potential of PLA as anti-biofilm compound against P. aeruginosa.
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Affiliation(s)
- Maitrayee Chatterjee
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India
| | - Sharon D'Morris
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India
| | - Vinod Paul
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India
| | - Sruthi Warrier
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India
| | - Anil Kumar Vasudevan
- Department of Microbiology, Amrita Institute of Medical Sciences and Research Centre, Amrita University, Cochin, Kerala, 682041, India
| | | | | | - Bindhu Paul-Prasanth
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India
| | - C Gopi Mohan
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India
| | - Raja Biswas
- Centre for Nanosciences and Molecular Medicine, Amrita University, Cochin, Kerala, 682041, India.
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Vanuopadath M, Nair D, Gopalakrishnan Nair B, Sadasivan Nair S. Post-translational Modifications of Proteins: Biomarkers and Therapeutic Targets for Diabetes Related Complications. CURR PROTEOMICS 2016. [DOI: 10.2174/1570164613666161031155258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Malvi P, Chaube B, Singh SV, Mohammad N, Pandey V, Vijayakumar MV, Radhakrishnan RM, Vanuopadath M, Nair SS, Nair BG, Bhat MK. Weight control interventions improve therapeutic efficacy of dacarbazine in melanoma by reversing obesity-induced drug resistance. Cancer Metab 2016; 4:21. [PMID: 27980732 PMCID: PMC5142287 DOI: 10.1186/s40170-016-0162-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Obesity-related cellular, metabolic, and molecular alterations have been shown to increase cancer risk and tumor progression and are associated with poorer therapeutic outcome in cancer patients. However, the impact of obesity and weight-control interventions on the therapeutic response in melanoma is poorly understood. METHODS High fat diet (HFD)-induced obese mouse model was used in this study to evaluate the outcome of dacarbazine (DTIC) therapy in melanoma. We employed LC-MS/MS to determine the quantity of the drug in tumor, and in various tissues. Unique in vitro approach was used to complement in vivo findings by culturing melanoma cells in either conditioned medium (CM) obtained from differentiated adipocytes or in serum collected from experimental mice. RESULTS We report that diet-induced obesity impairs the outcome of DTIC therapy and reduces overall survival in tumor-bearing mice. We provide evidence that obesity restricts the accessibility of DTIC to tumor tissue. Critically, upon curtailing adiposity, accumulation and efficacy of DTIC is significantly improved. Moreover, using appropriate in vitro approaches, we show that melanoma cells exhibit a drug-resistant phenotype when cultured in serum collected from diet-induced obese mice or in CM collected from 3T3-L1 adipocytes. The impaired therapeutic response to DTIC in obese state is mediated by fatty acid synthase (FASN), caveolin-1 (Cav-1), and P-glycoprotein (P-gp). The response to DTIC and overall survival were improved upon employing weight control interventions in the tumor-bearing HFD-fed (obese) mice. CONCLUSIONS This study indicates that obesity not only supports rapid melanoma progression but also impairs the outcome of chemotherapy, which can be improved upon employing weight control interventions. From clinically relevant point of view, our study exemplifies the importance of lifestyle interventions in the treatment of obesity-promoted cancers.
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Affiliation(s)
- Parmanand Malvi
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India
| | - Balkrishna Chaube
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India
| | - Shivendra Vikram Singh
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India
| | - Naoshad Mohammad
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India
| | - Vimal Pandey
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India ; Present address: Laboratory of Neuroscience, Department of Biotechnology and Bioinformatics, Hyderabad Central University, Hyderabad, 500 046 India
| | - Maleppillil Vavachan Vijayakumar
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India
| | | | - Muralidharan Vanuopadath
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, 690 525 India
| | - Sudarslal Sadasivan Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, 690 525 India
| | | | - Manoj Kumar Bhat
- Laboratory No. 6, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Ganeshkhind, Pune, 411 007 India
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Nair D, Vanuopadath M, Nair BG, Pai JG, Nair SS. Identification and characterization of a library of surfactins and fengycins from a marine endophytic Bacillus sp. J Basic Microbiol 2016; 56:1159-1172. [PMID: 27160506 DOI: 10.1002/jobm.201600029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/24/2016] [Indexed: 11/05/2022]
Abstract
An endophytic bacterial strain from a marine green alga, Ulva lactuca, was isolated and identified by 16S rRNA gene sequencing method. The bacterial isolate was found to secrete two major families of cyclic depsilipopeptides, surfactins, and fengycins. Sequencing of the isolated lipopeptides was carried out using the MSn data obtained from an electrospray ionization (ESI) ion trap mass spectrometer coupled to an HPLC system. The assigned sequences were confirmed by a chemical derivatization approach involving esterification followed by mass spectrometric analysis. Distinction of leucine residues from isoleucine was established through a combined electron transfer dissociation-collision-induced dissociation (ETD-CID) method. The fengycins described in this study were found to cause significant delay of growth of two plants, Vigna radiata (mung bean) and Oryza sativa (rice). To the best of our knowledge, this is the first study describing identification and characterization of cyclic peptides from an endophytic Bacillus sp. isolated from marine algae.
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Affiliation(s)
- Divya Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. Kollam, Kerala, India
| | | | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. Kollam, Kerala, India
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Mohammad N, Singh SV, Malvi P, Chaube B, Athavale D, Vanuopadath M, Nair SS, Nair B, Bhat MK. Strategy to enhance efficacy of doxorubicin in solid tumor cells by methyl-β-cyclodextrin: Involvement of p53 and Fas receptor ligand complex. Sci Rep 2015; 5:11853. [PMID: 26149967 PMCID: PMC4493576 DOI: 10.1038/srep11853] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/20/2015] [Indexed: 12/25/2022] Open
Abstract
Doxorubicin (DOX) is one of the preferred drugs for treating breast and liver cancers. However, its clinical application is limited due to severe side effects and the accompanying drug resistance. In this context, we investigated the effect on therapeutic efficacy of DOX by cholesterol depleting agent methyl-β-cyclodextrin (MCD), and explored the involvement of p53. MCD sensitizes MCF-7 and Hepa1–6 cells to DOX, Combination of MCD and marginal dose of DOX reduces the cell viability, and promoted apoptosis through induction of pro-apoptotic protein, Bax, activation of caspase-8 and caspase-7, down regulation of anti-apoptotic protein Bcl-2 and finally promoting PARP cleavage. Mechanistically, sensitization to DOX by MCD was due to the induction of FasR/FasL pathway through p53 activation. Furthermore, inhibition of p53 by pharmacological inhibitor pifithrin-α (PFT-α) or its specific siRNA attenuated p53 function and down-regulated FasR/FasL, thereby preventing cell death. Animal experiments were performed using C57BL/6J mouse isografted with Hepa1–6 cells. Tumor growth was retarded and survival increased in mice administered MCD together with DOX to as compared to either agent alone. Collectively, these results suggest that MCD enhances the sensitivity to DOX for which wild type p53 is an important determinant.
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Affiliation(s)
- Naoshad Mohammad
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune- 411007, India
| | - Shivendra Vikram Singh
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune- 411007, India
| | - Parmanand Malvi
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune- 411007, India
| | - Balkrishna Chaube
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune- 411007, India
| | - Dipti Athavale
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune- 411007, India
| | | | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam-690525, India
| | - Manoj Kumar Bhat
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune- 411007, India
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