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Qasemi M, Sur VP, Simonik O, Postlerova P, Skrobanek P, Hradec T, Boublikova L, Zamecnik L, Buchler T, Neuzil J, Komrskova K. Sperm mitochondria dysfunction in response to testicular cancer. Eur J Clin Invest 2024; 54:e14146. [PMID: 38069497 DOI: 10.1111/eci.14146] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 03/13/2024]
Abstract
Testicular cancer is the most common form of cancer in young men of reproductive age and its incidence is increasing globally. With the currently successful treatment and 95% survival rate, there is a need for deeper understanding of testicular cancer-related infertility. Most patients with testicular cancer experience semen abnormalities prior to cancer therapy. However, the exact mechanism of the effect of testicular cancer on sperm anomalies is not known. Mitochondria are organelles that play a crucial role in both tumorigenesis and spermatogenesis and their malfunction may be an important factor resulting in sperm abnormalities in testicular cancer patients. Within the scope of this review, we will discuss current knowledge of testicular cancer-related alterations in the ATP production pathway, a possible pathophysiological switch from oxidative phosphorylation (OXPHOS) to glycolysis, as well as the role of oxidative stress promoting sperm dysfunction. In this regard, the review provides a summary of the impact of testicular cancer on sperm quality as a possible consequence of impaired mitochondrial function including the energy metabolic pathways that are known to be altered in the sperm of testicular cancer patients.
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Affiliation(s)
- Maryam Qasemi
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Pavla Postlerova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Praha, Czech Republic
| | - Pavel Skrobanek
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czech Republic
| | - Tomas Hradec
- Department of Urology, General University Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Boublikova
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czech Republic
| | - Libor Zamecnik
- Department of Urology, General University Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czech Republic
- Department of Oncology, Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Jiri Neuzil
- Laboratory of Molecular Therapy, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
- School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Frolikova M, Sur VP, Novotny I, Blazikova M, Vondrakova J, Simonik O, Ded L, Valaskova E, Koptasikova L, Benda A, Postlerova P, Horvath O, Komrskova K. Juno and CD9 protein network organization in oolemma of mouse oocyte. Front Cell Dev Biol 2023; 11:1110681. [PMID: 37635875 PMCID: PMC10450504 DOI: 10.3389/fcell.2023.1110681] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Juno and CD9 protein, expressed in oolemma, are known to be essential for sperm-oocyte binding and fusion. Although evidence exists that these two proteins cooperate, their interaction has not yet been demonstrated. Here in, we present Juno and CD9 mutual localization over the surface of mouse metaphase II oocytes captured using the 3D STED super-resolution technique. The precise localization of examined proteins was identified in different compartments of oolemma such as the microvillar membrane, planar membrane between individual microvilli, and the membrane of microvilli-free region. Observed variance in localization of Juno and CD9 was confirmed by analysis of transmission and scanning electron microscopy images, which showed a significant difference in the presence of proteins between selected membrane compartments. Colocalization analysis of super-resolution images based on Pearson's correlation coefficient supported evidence of Juno and CD9 mutual position in the oolemma, which was identified by proximity ligation assay. Importantly, the interaction between Juno and CD9 was detected by co-immunoprecipitation and mass spectrometry in HEK293T/17 transfected cell line. For better understanding of experimental data, mouse Juno and CD9 3D structure were prepared by comparative homology modelling and several protein-protein flexible sidechain dockings were performed using the ClusPro server. The dynamic state of the proteins was studied in real-time at atomic level by molecular dynamics (MD) simulation. Docking and MD simulation predicted Juno-CD9 interactions and stability also suggesting an interactive mechanism. Using the multiscale approach, we detected close proximity of Juno and CD9 within microvillar oolemma however, not in the planar membrane or microvilli-free region. Our findings show yet unidentified Juno and CD9 interaction within the mouse oolemma protein network prior to sperm attachment. These results suggest that a Juno and CD9 interactive network could assist in primary Juno binding to sperm Izumo1 as a prerequisite to subsequent gamete membrane fusion.
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Affiliation(s)
- Michaela Frolikova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Ivan Novotny
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Michaela Blazikova
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Vondrakova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Lukas Ded
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Eliska Valaskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Lenka Koptasikova
- Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, Vestec, Czechia
| | - Ales Benda
- Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, Vestec, Czechia
| | - Pavla Postlerova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, University of Life Sciences Prague, Prague, Czechia
| | - Ondrej Horvath
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
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Bharati R, Sen MK, Kumar R, Gupta A, Sur VP, Melnikovová I, Fernández-Cusimamani E. Selection and Validation of the Most Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Salvia rosmarinus under In Vitro Conditions. Plants (Basel) 2022; 11:2878. [PMID: 36365331 PMCID: PMC9655146 DOI: 10.3390/plants11212878] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Salvia rosmarinus L. (rosemary) is known to have a wide range of pharmacological effects including antidiabetic, anticarcinogenic, and antitumorigenic properties owing to its secondary metabolites. Studies aiming to elevate these metabolites have utilized various elicitors and stresses under in vitro conditions, although underlying molecular mechanisms remain unexplored. Gene expression studies using RT-qPCR might provide valuable information regarding how plant and plant cells interact and perceive various treatments and elicitors. However, despite being able to calculate accurate fold changes, the accuracy of the RT-qPCR data highly depends on the expression of reference genes. To the best of our knowledge, there is no information available on the stable reference genes in rosemary under in vitro conditions. Thus, in this paper, we assessed the stability of seven commonly used reference genes under different elicitor and stress conditions using RT-qPCR. Thereafter, the five most commonly used software and algorithms (comparative ΔCt, BestKeeper, NormFinder, geNorm, and RefFinder) were used to rank the candidates based on their expression stabilities. In conclusion, we recommend using a combination of F1-ATPase, ATP synthase and ACCase to normalize the gene expression experiments in rosemary under in vitro conditions. The selected reference genes were verified using 4-coumarate-CoA ligase, a pharmacologically important gene, whose expression might alter under nanoparticle treatment. Additionally, reference genes for several plant tissues, elicitors, and stresses are also proposed. The conclusions obtained from this current study will accelerate the future molecular work in S. rosmarinus and other related species.
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Affiliation(s)
- Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Ram Kumar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Ingrid Melnikovová
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Eloy Fernández-Cusimamani
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
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Sur VP, Simonik O, Novotna M, Mazumdar A, Liska F, Vimberg V, Komrskova K. Dynamic study of small toxic hydrophobic proteins PepA1 and PepG1 of Staphylococcus aureus. Int J Biol Macromol 2022; 219:1360-1371. [PMID: 35932805 DOI: 10.1016/j.ijbiomac.2022.07.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
Toxin-antitoxin (TA) systems are small genetic elements which encode toxin proteins that interfere with vital cellular functions. PepA1 and PepG1 toxin proteins, known also as SprA1 and SprG1, are type I TA. In Staphylococcus aureus (S. aureus), their expression without the antitoxin counterparts (SprA1AS and SprF1), is lethal to the pathogen. Molecular Dynamics (MD) simulation was performed for PepA1 and PepG1 to understand their dynamic state, conformational changes, and their toxicity. The protein structures were constructed and used for MD simulation and the conformational changes, stability, flexibility, fluctuations, hydrophobicity, and role of their dynamic state on function prediction were studied extensively by GROMACS MD simulation analysis tools. In silico study indicated that the PepA1 and PepG1 proteins change their structural conformation from an open to closed state where PepA1 conformational changes were faster (10 ns) than PepG1 (20 ns) while PepG1 exerted more stability and flexibility than PepA1. According to SASA values, PepG1 is more hydrophobic than the PepA1 and forms fewer hydrogen bonds than PepA1. The in vivo study with PepA1 and PepG1 proteins provided evidence that both the conformation changes between the open and closed states and the amino acid sequence are crucial for peptide toxicity.
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Affiliation(s)
- Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Michaela Novotna
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Aninda Mazumdar
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Frantisek Liska
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Vladimir Vimberg
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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Kumar R, Mazakova J, Ali A, Sur VP, Sen MK, Bolton MD, Manasova M, Rysanek P, Zouhar M. Characterization of the Molecular Mechanisms of Resistance against DMI Fungicides in Cercospora beticola Populations from the Czech Republic. J Fungi (Basel) 2021; 7:1062. [PMID: 34947044 PMCID: PMC8706352 DOI: 10.3390/jof7121062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/20/2022] Open
Abstract
Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is the most important foliar pathogen of sugar beet worldwide. Extensive reliance on fungicides to manage CLS has resulted in the evolution of fungicide resistance in C. beticola worldwide, including populations in the Czech Republic. One important class of fungicides used to manage CLS is the sterol demethylation inhibitors (DMI). The aim of our study was to assess DMI resistance in C. beticola from the Czech Republic and elucidate the molecular basis of DMI resistance in this population. A total of 50 isolates were collected in 2018 and 2019 from the major sugar beet growing regions of the Czech Republic and assessed for in vitro sensitivity to the DMI fungicides propiconazole, prochloraz, and epoxiconazole. These analyses identified three strains that exhibited 50% effective concentration (EC50) values > 1.0 μg mL-1 against respective fungicides, which were therefore considered resistant. In contrast, strains that exhibited lowest EC50 values were considered sensitive. To explore the molecular basis of resistance in these three strains, the cytochrome P450-dependent sterol 14α-demethylase (Cyp51) gene was sequenced. Sequence analysis identified a Y464S mutation in all three resistant strains. To assess whether Cyp51 gene expression may play a role in DMI resistance, selected strains were grown in vitro with and without fungicide treatment. These analyses indicated that Cyp51 gene expression was significantly induced after fungicide treatment. Thus, we conclude that Y464S point mutation along with induced Cyp51 gene overexpression is likely responsible for resistance against DMI fungicides in C. beticola from the Czech Republic.
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Affiliation(s)
- Ram Kumar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (R.K.); (J.M.); (A.A.); (M.M.); (P.R.)
| | - Jana Mazakova
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (R.K.); (J.M.); (A.A.); (M.M.); (P.R.)
| | - Asad Ali
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (R.K.); (J.M.); (A.A.); (M.M.); (P.R.)
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic;
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Melvin D. Bolton
- Northern Crop Science Laboratory, United States Department of Agriculture, 1307 18th St N, Fargo, ND 58102, USA;
| | - Marie Manasova
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (R.K.); (J.M.); (A.A.); (M.M.); (P.R.)
| | - Pavel Rysanek
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (R.K.); (J.M.); (A.A.); (M.M.); (P.R.)
| | - Miloslav Zouhar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (R.K.); (J.M.); (A.A.); (M.M.); (P.R.)
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Sur VP, Sen MK, Komrskova K. In Silico Identification and Validation of Organic Triazole Based Ligands as Potential Inhibitory Drug Compounds of SARS-CoV-2 Main Protease. Molecules 2021; 26:6199. [PMID: 34684780 PMCID: PMC8541586 DOI: 10.3390/molecules26206199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
The SARS-CoV-2 virus is highly contagious to humans and has caused a pandemic of global proportions. Despite worldwide research efforts, efficient targeted therapies against the virus are still lacking. With the ready availability of the macromolecular structures of coronavirus and its known variants, the search for anti-SARS-CoV-2 therapeutics through in silico analysis has become a highly promising field of research. In this study, we investigate the inhibiting potentialities of triazole-based compounds against the SARS-CoV-2 main protease (Mpro). The SARS-CoV-2 main protease (Mpro) is known to play a prominent role in the processing of polyproteins that are translated from the viral RNA. Compounds were pre-screened from 171 candidates (collected from the DrugBank database). The results showed that four candidates (Bemcentinib, Bisoctrizole, PYIITM, and NIPFC) had high binding affinity values and had the potential to interrupt the main protease (Mpro) activities of the SARS-CoV-2 virus. The pharmacokinetic parameters of these candidates were assessed and through molecular dynamic (MD) simulation their stability, interaction, and conformation were analyzed. In summary, this study identified the most suitable compounds for targeting Mpro, and we recommend using these compounds as potential drug molecules against SARS-CoV-2 after follow up studies.
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Affiliation(s)
- Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV—Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic;
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 1176, 165 00 Prague, Czech Republic;
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV—Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic;
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
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Mazumdar A, Haddad Y, Sur VP, Milosavljevic V, Bhowmick S, Michalkova H, Guran R, Vesely R, Moulick A. Characterization and in vitro Analysis of Probiotic-Derived Peptides Against Multi Drug Resistance Bacterial Infections. Front Microbiol 2020; 11:1963. [PMID: 32983007 PMCID: PMC7477325 DOI: 10.3389/fmicb.2020.01963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/06/2020] [Accepted: 07/24/2020] [Indexed: 11/21/2022] Open
Abstract
An inexorable switch from antibiotics has become a major desideratum to overcome antibiotic resistance. Bacteriocin from Lactobacillus casei, a cardinal probiotic was used to design novel antibacterial peptides named as Probiotic Bacteriocin Derived and Modified (PBDM) peptides (PBDM1: YKWFAHLIKGLC and PBDM2: YKWFRHLIKKLC). The loop-shaped 3D structure of peptides was characterized in silico via molecular dynamics simulation as well as biophysically via spectroscopic methods. Thereafter, in vitro results against multidrug resistant bacterial strains and hospital samples demonstrated the strong antimicrobial activity of PBDM peptides. Further, in vivo studies with PBDM peptides showed downright recovery of balb/c mice from Vancomycin Resistant Staphylococcus aureus (VRSA) infection to its healthy condition. Thereafter, in vitro study with human epithelial cells showed no significant cytotoxic effects with high biocompatibility and good hemocompatibility. In conclusion, PBDM peptides displayed significant antibacterial activity against certain drug resistant bacteria which cause infections in human beings. Future analysis are required to unveil its mechanism of action in order to execute it as an alternative to antibiotics.
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Affiliation(s)
- Aninda Mazumdar
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Vishma Pratap Sur
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Sukanya Bhowmick
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Hana Michalkova
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Roman Guran
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Radek Vesely
- Department of Traumatology at the Medical Faculty, Masaryk University and Trauma Hospital of Brno, Brno, Czechia
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.,Central European Institute of Technology, Brno University of Technology, Brno, Czechia
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Sur VP, Mazumdar A, Kopel P, Mukherjee S, Vítek P, Michalkova H, Vaculovičová M, Moulick A. A Novel Ruthenium Based Coordination Compound Against Pathogenic Bacteria. Int J Mol Sci 2020; 21:E2656. [PMID: 32290291 PMCID: PMC7178087 DOI: 10.3390/ijms21072656] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
The current epidemic of antibiotic-resistant infections urges to develop alternatives to less-effective antibiotics. To assess anti-bacterial potential, a novel coordinate compound (RU-S4) was synthesized using ruthenium-Schiff base-benzimidazole ligand, where ruthenium chloride was used as the central atom. RU-S4 was characterized by scanning electron microscope (SEM), energy-dispersive X-ray spectroscopy (EDS), and Raman spectroscopy. Antibacterial effect of RU-S4 was studied against Staphylococcus aureus (NCTC 8511), vancomycin-resistant Staphylococcus aureus (VRSA) (CCM 1767), methicillin-resistant Staphylococcus aureus (MRSA) (ST239: SCCmecIIIA), and hospital isolate Staphylococcus epidermidis. The antibacterial activity of RU-S4 was checked by growth curve analysis and the outcome was supported by optical microscopy imaging and fluorescence LIVE/DEAD cell imaging. In vivo (balb/c mice) infection model prepared with VRSA (CCM 1767) and treated with RU-S4. In our experimental conditions, all infected mice were cured. The interaction of coordination compound with bacterial cells were further confirmed by cryo-scanning electron microscope (Cryo-SEM). RU-S4 was completely non-toxic against mammalian cells and in mice and subsequently treated with synthesized RU-S4.
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Affiliation(s)
- Vishma Pratap Sur
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00 Brno, Czech Republic; (A.M.); (S.M.); (H.M.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, CZ-61200 Brno, Czech Republic
| | - Aninda Mazumdar
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00 Brno, Czech Republic; (A.M.); (S.M.); (H.M.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, CZ-61200 Brno, Czech Republic
| | - Pavel Kopel
- Department of Inorganic Chemistry, Faculty of Science, Palacky University, CZ-771 46 Olomouc, Czech Republic;
| | - Soumajit Mukherjee
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00 Brno, Czech Republic; (A.M.); (S.M.); (H.M.); (M.V.)
| | - Petr Vítek
- Global Change Research Institute of the Czech Academy of Sciences, CZ- 603 00 Brno, Czech Republic;
| | - Hana Michalkova
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00 Brno, Czech Republic; (A.M.); (S.M.); (H.M.); (M.V.)
| | - Markéta Vaculovičová
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00 Brno, Czech Republic; (A.M.); (S.M.); (H.M.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, CZ-61200 Brno, Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00 Brno, Czech Republic; (A.M.); (S.M.); (H.M.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, CZ-61200 Brno, Czech Republic
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Ghosh T, Maity N, Sur VP, Konar A, Hazra S. Mitigating fibrosis-An impediment to corneal re-innervation following lamellar flap surgery. Exp Eye Res 2020; 194:108009. [PMID: 32205135 DOI: 10.1016/j.exer.2020.108009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/20/2020] [Accepted: 03/15/2020] [Indexed: 10/24/2022]
Abstract
Restoration of corneal sensitivity is of utmost importance to maintain corneal homeostasis following any injury or insult, for which, both corneal nerve regeneration and re-innervation are essential. Fibrosis poses a major impediment for re-innervation. We have in this study evaluated the influence of various nerve growth factors and corneal fibrosis on corneal nerve regeneration and reinnervation following lamellar flap surgery (LFS) and its modulation using antifibrotic drug pirfenidone. To achieve this, trigeminal ganglion cells were treated with pirfenidone, NGF, and NT-3 to evaluate their effect on trigeminal cell neurite growth. Following LFS, the gene expression of nerve growth factors NGF, BDNF and NT-3, Gap 43, Nogo-A and profibrotic factors Tenascin C, TGF-beta 1 were evaluated with and without pirfenidone. Wound fibrosis and corneal nerve regeneration using pirfenidone following LFS were evaluated by staining whole corneal mounts with α SMA and β tubulin 3. Safety of NGF and pirfenidone topical drops in normal unoperated cornea and its efficacy in enhancing corneal healing was evaluated following LFS. Our study shows, pirfenidone did not influence trigeminal cell neurite elongation; NGF and NT-3 significantly enhanced trigeminal cell neurite elongation. NT-3 also significantly increased neurite branching. There was significant increase in the gene expression of NGF, BDNF, NT-3, Gap- 43, TGF beta-1, Tenascin C, Nogo-A genes in the operated cornea compared to normal cornea, treatment of operated corneas with pirfenidone prevented the increased expression of these genes except Gap 43 which remained unchanged. The treatment of operated eyes with combination of NGF and pirfenidone positively influenced corneal healing compared to treatment with NGF alone, and had no adverse influence on the cornea. Pirfenidone appreciably reduced corneal fibrosis which aided in re-innervation. Both NGF and NT3 positively influence trigeminal neurite elongation. NGF and pirfenidone have complementary influence on corneal wound healing.
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Affiliation(s)
- Tanushri Ghosh
- Dept of Veterinary Surgery & Radiology, West Bengal University of Animal & Fishery Sciences, 37& 68 Khudiram Bose Sarani, Kolkata, 700037, India
| | - Namrata Maity
- Dept of Veterinary Surgery & Radiology, West Bengal University of Animal & Fishery Sciences, 37& 68 Khudiram Bose Sarani, Kolkata, 700037, India
| | | | | | - Sarbani Hazra
- Dept of Veterinary Surgery & Radiology, West Bengal University of Animal & Fishery Sciences, 37& 68 Khudiram Bose Sarani, Kolkata, 700037, India.
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Sur VP, Kominkova M, Buchtova Z, Dolezelikova K, Zitka O, Moulick A. CdSe QD Biosynthesis in Yeast Using Tryptone-Enriched Media and Their Conjugation with a Peptide Hecate for Bacterial Detection and Killing. Nanomaterials (Basel) 2019; 9:nano9101463. [PMID: 31623115 PMCID: PMC6835635 DOI: 10.3390/nano9101463] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
The physical and chemical synthesis methods of quantum dots (QDs) are generally unfavorable for biological applications. To overcome this limitation, the development of a novel “green” route to produce highly-fluorescent CdSe QDs constitutes a promising substitute approach. In the present work, CdSe QDs were biosynthesized in yeast Saccharomyces cerevisiae using a novel method, where we showed for the first time that the concentration of tryptone highly affects the synthesis process. The optimum concentration of tryptone was found to be 25 g/L for the highest yield. Different methods were used to optimize the QD extraction from yeast, and the best method was found to be by denaturation at 80 °C along with an ultrasound needle. Multiple physical characterizations including transmission electron microscopy (TEM), dynamic light scattering (DLS), energy-dispersive X-ray spectroscopy (EDX), and spectrophotometry confirmed the optical features size and shape distribution of the QDs. We showed that the novel conjugate of the CdSe QDs and a cell-penetrating peptide (hecate) can detect bacterial cells very efficiently under a fluorescent microscope. The conjugate also showed strong antibacterial activity against vancomycin-resistant Staphylococcus aureus (VRSA), methicillin-resistant Staphylococcus aureus (MRSA), and Escherichia coli, which may help us to cope with the problem of rising antibiotic resistance.
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Affiliation(s)
- Vishma Pratap Sur
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-61300 Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 61200 Brno, Czech Republic.
| | - Marketa Kominkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-61300 Brno, Czech Republic.
| | - Zaneta Buchtova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-61300 Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 61200 Brno, Czech Republic.
| | - Kristyna Dolezelikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-61300 Brno, Czech Republic.
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-61300 Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 61200 Brno, Czech Republic.
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-61300 Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 61200 Brno, Czech Republic.
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Jelinkova P, Mazumdar A, Sur VP, Kociova S, Dolezelikova K, Jimenez AMJ, Koudelkova Z, Mishra PK, Smerkova K, Heger Z, Vaculovicova M, Moulick A, Adam V. Nanoparticle-drug conjugates treating bacterial infections. J Control Release 2019; 307:166-185. [DOI: 10.1016/j.jconrel.2019.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
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Jelinkova P, Splichal Z, Jimenez AMJ, Haddad Y, Mazumdar A, Sur VP, Milosavljevic V, Kopel P, Buchtelova H, Guran R, Zitka O, Richtera L, Hegerova D, Heger Z, Moulick A, Adam V. Novel vancomycin-peptide conjugate as potent antibacterial agent against vancomycin-resistant Staphylococcus aureus. Infect Drug Resist 2018; 11:1807-1817. [PMID: 30349337 PMCID: PMC6190637 DOI: 10.2147/idr.s160975] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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] [Indexed: 01/18/2023] Open
Abstract
Background Increase in vancomycin (Van)-resistant bacterial strains including vancomycin-resistant Staphylococcus aureus (VRSA) and lack of new effective antibiotics have become a formidable health problem. Materials and methods We designed a new conjugate composed of Van and a peptide Hecate (Hec; Van/Hec), and its potential antimicrobial activity was evaluated. Results Results from disk diffusion test, time-kill assay, determination of minimum inhibitory concentration (MIC), microscopy, and comet assay showed strong antimicrobial effects of Van/Hec against wild-type, methicillin-resistant Staphylococcus aureus (MRSA) and VRSA. Microscopy revealed that the exposure to Van/Hec results in disruption of bacterial cell integrity in all tested strains, which was not observed in case of Van or Hec alone. Conclusion Overall, we showed that the preparation of conjugates from antibiotics and biologically active peptides could help us to overcome the limitation of the use of antibiotic in the treatment of infections caused by multidrug-resistant bacteria.
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Affiliation(s)
- Pavlina Jelinkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic,
| | - Zbynek Splichal
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Ana Maria Jimenez Jimenez
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Aninda Mazumdar
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Vishma Pratap Sur
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Hana Buchtelova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic,
| | - Roman Guran
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Dagmar Hegerova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska, Brno, Czech Republic, .,Central European Institute of Technology, Brno University of Technology, Purkynova, Brno, Czech Republic,
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Gupta PSS, Banerjee S, Islam RNU, Sur VP, Bandyopadhyay AK. Substitutional Analysis of Orthologous Protein Families Using BLOCKS. Bioinformation 2017; 13:1-7. [PMID: 28479743 PMCID: PMC5405086 DOI: 10.6026/97320630013001] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/27/2016] [Indexed: 11/29/2022] Open
Abstract
Orthologous proteins, form due to divergence of parental sequence, perform similar function under different environmental and
biological conditions. Amino acid changes at locus specific positions form hetero-pairs whose role in BLOCK evolution is yet to be
understood. We involve eight protein BLOCKs of known divergence rate to gain insight into the role of hetero-pairs in evolution. Our
procedure APBEST uses BLOCK-FASTA file to extract BLOCK specific evolutionary parameters such as dominantly used hetero-pair
(D), usage of hetero-pairs (E), non-conservative to conservative substitution ratio (R), maximally-diverse residue (MDR), residue (RD)
and class (CD) specific diversity. All these parameters show BLOCK specific variation. Conservative nature of D points towards
restoration of function of BLOCK. While E sets the upper-limit of usage of hereto-pairs, strong correlation of R with divergence-rate
indicates that the later is directly dependent on non-conservative substitutions. The observation that MDR, measure of positional
diversity, occupy very limited positions in BLOCK indicates accommodation of diversity is positionally restricted. Overall, the study
extract observed hetero-pair related quantitative and multi-parametric details of BLOCK, which finds application in evolutionary
biology.
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Affiliation(s)
- Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Vishma Pratap Sur
- Indian Institute of Chemical Biology, Animal House (IICB), Kolkata, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Khanum BNMK, Guha R, Sur VP, Nandi S, Basak SK, Konar A, Hazra S. Pirfenidone inhibits post-traumatic proliferative vitreoretinopathy. Eye (Lond) 2017; 31:1317-1328. [PMID: 28304388 DOI: 10.1038/eye.2017.21] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/09/2017] [Indexed: 12/13/2022] Open
Abstract
PurposeThe purpose of the study was to evaluate the efficacy and safety of intravitreal pirfenidone for inhibition of proliferative vitreoretinopathy (PVR) in a model of penetrating ocular injury.Patients and methodsPenetrating trauma was induced on the retina of rabbit and treated either with 0.1 ml of phosphate-buffered saline (PBS) or 0.1 ml of 0.5% pirfenidone, and development of PVR was evaluated clinically and graded after 1 month. Histopathology and immunohistochemistry with transforming growth factor beta (TGFβ), alpha smooth muscle actin (αSMA), and collagen-1 were performed to assess the fibrotic changes. Expression of cytokines in the vitro-retinal tissues at different time points following pirfenidone and PBS injection was examined by RT-PCR. Availability of pirfenidone in the vitreous of rabbit at various time points was determined by high-performance liquid chromatography following injection of 0.1 ml of 0.5% pirfenidone. In normal rabbit eye, 0.1 ml of 0.5% pirfenidone was injected to evaluate any toxic effect.ResultsClinical assessment and grading revealed prevention of PVR formation in pirfenidone-treated animals, gross histology, and histopathology confirmed the observation. Immunohistochemistry showed prevention in the expression of collagen-I, αSMA, and TGFβ in the pirfenidone-treated eyes compared to the PBS-treated eyes. Pirfenidone inhibited increased gene expression of cytokines observed in control eyes. Pirfenidone could be detected up to 48 h in the vitreous of rabbit eye following single intravitreal injection. Pirfenidone did not show any adverse effect following intravitreal injection; eyes were devoid of any abnormal clinical sign, intraocular pressure, and electroretinography did not show any significant change and histology of retina remained unchanged.ConclusionThis animal study shows that pirfenidone might be a potential therapy for PVR. Further clinical study will be useful to evaluate the clinical application of pirfenidone.
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Affiliation(s)
- B N M K Khanum
- Department of Veterinary Surgery &Radiology, West Bengal University of Animal &Fishery Sciences, Kolkata, India
| | - R Guha
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - V P Sur
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - S Nandi
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - A Konar
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - S Hazra
- Department of Veterinary Surgery &Radiology, West Bengal University of Animal &Fishery Sciences, Kolkata, India
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Banerjee S, Gupta PSS, Nayek A, Das S, Sur VP, Seth P, Islam RNU, Bandyopadhyay AK. PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2. Bioinformation 2015; 11:366-8. [PMID: 26339154 PMCID: PMC4546997 DOI: 10.6026/97320630011366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 05/08/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 11/23/2022] Open
Abstract
Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of
sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO
and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution
(PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides
users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of
Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized
outputs in excel format along with detailed methodology. The program package contains documentation describing application of
methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics.
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Affiliation(s)
| | | | | | - Sunit Das
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Vishma Pratap Sur
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Pratyay Seth
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Nayek A, Gupta PSS, Banerjee S, Sur VP, Seth P, Das S, Islam RNU, Bandyopadhyay AK. ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2. Bioinformation 2015; 11:413-5. [PMID: 26420923 PMCID: PMC4574125 DOI: 10.6026/97320630011413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 08/05/2015] [Accepted: 08/17/2015] [Indexed: 12/02/2022] Open
Abstract
Component (bridge: ΔΔGbrd, background: ΔΔGprot, desolvation: ΔΔGdsolv) and net (ΔΔGnet) energy-terms of salt-bridge-structure
(SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS)
method. While the procedure reports gross energy terms (Kcal Mol-1), report on bond-multiplicity corrected normalized energyterms
(Kcal Mol-1 Bond-1) along with their accessibility (ASA) in monomer, isolated-SBS (ISBS) and networked-SBS (NSBS) format
would be very useful for statistical comparison among SBSs and understanding their location in protein structure. In this end,
ADSBET2 potentially incorporates these features along with additional model for side-chain. Gross and normalized energy-terms
are redirected in monomer, ISBS and NSBS format along with their ASA informations. It works on any number of SBSs for any
number of structure files present in a database. Taken together, ADSBET2 has been suitable for statistical analyses of SBSs
energetics and finds applications in protein engineering and structural bioinformatics.
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Affiliation(s)
| | | | | | - Vishma Pratap Sur
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Pratyay Seth
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Sunit Das
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal Kumar Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Gupta PSS, Nayek A, Banerjee S, Seth P, Das S, Sur VP, Roy C, Bandyopadhyay AK. SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2. Bioinformation 2015; 11:39-42. [PMID: 25780279 PMCID: PMC4349938 DOI: 10.6026/97320630011039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 10/25/2014] [Accepted: 12/14/2014] [Indexed: 11/24/2022] Open
Abstract
Specific electrostatics (i.e. salt-bridge) includes both local and non-local interactions that contribute to the overall stability of
proteins. It has been shown that a salt-bridge could either be buried or exposed, networked or isolated, hydrogen-bonded or nonhydrogen
bonded, in secondary-structure or in coil, formed by single or multiple bonds. Further it could also participates either in
intra- or inter-dipole interactions with preference in orientation either for basic residue at N-terminal (orientation-I) or acidic
residue at N-terminal (orientation-II). In this context SBION2 is unique in that it reports above mentioned binary items in excel
format along with details on intra and inter-dipole interactions and orientations. These results are suitable for post run statistical
analyses involving large datasets. Reports are also made on protein-protein interactions, intervening residue distances and general
residue specific salt-bridge details. A ready to use compact supplementary table is also produced. The program runs in three
alternative modes. Each mode works on any number of structure files with any number of chains at any given atomic distance of
ion-pair. Thus SBION2 provides intricate details on salt-bridges and finds application in structural bioinformatics.
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Affiliation(s)
| | | | | | - Pratyay Seth
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
| | - Sunit Das
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
| | - Vishma Pratap Sur
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
| | - Chittran Roy
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
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