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James JJ, Sandhya KV, Sridhar KN, Sudarson S, Basavaraj BV, Bharath S. Proteomic Characterization of Human Placenta: Insights into Potential Therapeutic Applications for Osteoarthritis. AAPS PharmSciTech 2024; 25:139. [PMID: 38890179 DOI: 10.1208/s12249-024-02851-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
Biologics have become increasingly prominent as therapeutics in recent years due to their innate immune-privileged nature, biocompatibility, and high levels of protein biofactors. The aim of the study is to characterise the biologic, lyophilized human placenta (LHP) and explore its therapeutic potential for osteoarthritis (OA). The presence of six bioactive constituents that regulate cell-extracellular matrix interaction was identified by liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS). Metalloproteinase inhibitor 3 (TIMP3), alpha-1 anti-trypsin (a1AT), basic fibroblast growth factor (bFGF), and transforming growth factor β1 (TGFβ1) were detected and quantified using ELISA. The total protein content present in LHP by Bradford assay was found to be 409.35 ± 0.005 μg/ml. The analytical techniques such as Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR), solid state carbon-13 Nuclear Magnetic Resonance (ssC13 NMR) spectroscopy, and Differential Scanning Calorimetry (DSC) revealed the secondary structure and conformational stability of LHP. X-Ray diffraction (XRD) studies showed its amorphous nature. Bioactivity assessment of LHP was performed in human keratinocytes (HaCaT) and human dermal fibroblasts (HDF) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The LHP was highly proliferative against skin cells and non-toxic, based on the findings of the bioactivity assay. LHP has the potential to be used as a therapeutic agent for OA, as its characterisation unveiled its physical stability, significant concentration of bioactive components that are pertinent to cartilage repair and its conformational stability.
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Affiliation(s)
- Jithu Jerin James
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India
| | - K V Sandhya
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India.
| | - K N Sridhar
- Cancyte Technologies Pvt Ltd, Sri Shankara Research Centre, Rangadore Memorial Hospital, Shankarapuram, Bengaluru, India
| | - S Sudarson
- Cancyte Technologies Pvt Ltd, Sri Shankara Research Centre, Rangadore Memorial Hospital, Shankarapuram, Bengaluru, India
| | - B V Basavaraj
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India
| | - S Bharath
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India
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Sneha, Pandey JP, Pandey DM. Evaluating the role of trypsin in silk degumming: An in silico approach. J Biotechnol 2022; 359:35-47. [PMID: 36126805 DOI: 10.1016/j.jbiotec.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022]
Abstract
The trypsin being universal enzyme forming family of proteases catalyzes the hydrolysis of proteins into amino acids and regenerates the serine hydroxyl an active site. The trypsin enzyme from D. saccharalis, uses sericin as its preferred substrate. Presence of catalytic triad (serine, aspartic acid and histidine) at the substrate binding site of this enzyme is very important for the catalytic activity. In the current study, the interacting mechanism between the substrate sericin protein and enzyme trypsin protein were explored by integrating various computational approaches including physico-chemical properties, biophysical properties, dynamics, gene ontology, molecular docking, protein - protein interactions, binding free energy calculation and structural motifs were studied. The evolutionary study performed by MEGA X showed that trypsin protein sequence (ALE15212.1) is closely related to cocoonase protein sequence (ADG26770.1) from Antheraea pernyi. 3-D models of trypsin and sericin proteins were predicted using I-TASSER and further validated by PROCHECK, and ProSAweb softwares. The predicted trypsin structure model was assigned E.C. no. 3.4.21.4 which refers hydrolytic mechanism. Gene Ontology predicted by QuickGO showed that trypsin has serine hydrolase activity (GO: 00017171), and part of proteolysis (GO: 0006508) as well as protein metabolic process (GO:0019538) actvity. Molecular docking studies between trypsin and sericin proteins were conducted by the HADDOCK 2.4 having best docked protein complex with Z-score - 1.9. 2D and 3D protein-protein interaction was performed with LIGPLOT+ and HAWKDOCK, PDBsum, respectively. The amino acid residues interacting across proteins interface are sericin_chain A representing "Ser133, Tyr214, Thr188, Thr243, Ser225, Ser151, Ser156, His294, Arg293, Gly296″ and trypsin_chain B "Lys120, Tyr246, Asn119, Glu239, Ser62, Tyr194, Ile197, Ser171, Tyr169, Gly170″. Based on our results trypsin shows similarity with cocoonase and presumably trypsin can be used as an alternative source in cocoon degumming.
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Affiliation(s)
- Sneha
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
| | - Jay Prakash Pandey
- Central Tasar Research and Training Institute, Piska-Nagri, Ranchi, Jharkhand 835303, India.
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
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Raina D, Khan FG, Tiwari H, Sangwan PL, Nargotra A, Kumar V, Khan IA, Saran S. Boswellic acids, as novel inhibitor targeting peptidoglycan biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) in Escherichia coli. Arch Microbiol 2022; 204:472. [PMID: 35819545 DOI: 10.1007/s00203-022-03066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an essential cytosolic enzyme in the biosynthesis of peptidoglycan. It becomes a potential bacterial target for screening promising antibacterial compounds as it is associated with the early phases of peptidoglycan production. MurA enzyme is conserved and necessary for bacterial viability with no mammalian homolog, which is a well-proven therapeutic research target. The present study reports the natural compounds from Boswellia serrata targeting the MurA enzyme. The identified inhibitors against MurA Escherichia coli (E. coli): β-boswellic acid (IC50 33.65 µM), Acetyl-β-boswellic acid (IC50 30.17 µM), and Acetyl-11-keto-β-boswellic acid (IC50 37.67 µM). Inhibitors showed a fourfold decrease in IC50 values on pre-incubation with substrate-UDP-N-acetyl-glucosamine (UDP-GlcNAc). Mode-of-inhibition studies revealed their uncompetitive nature with both the substrates. Although these boswellic acids have been explored for their pharmacological potential, this is the first study reporting these compounds' E. coli MurA inhibiting potential.
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Affiliation(s)
- Diksha Raina
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Fermentation Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Farrah Gul Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Harshita Tiwari
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Payare L Sangwan
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Amit Nargotra
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Vinod Kumar
- Fermentation Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India.
| | - Saurabh Saran
- Fermentation Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India.
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Manhas RS, Tiwari H, Noor M, Ahmed A, Vishwakarma J, Tripathi RBM, Ramachandran R, Madishetti S, Mukherjee D, Nargotra A, Chaubey A. Setomimycin as a potential molecule for COVID‑19 target: in silico approach and in vitro validation. Mol Divers 2022; 27:619-633. [PMID: 35622309 PMCID: PMC9136828 DOI: 10.1007/s11030-022-10441-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/07/2022] [Indexed: 01/18/2023]
Abstract
Abstract COVID-19 pandemic caused by the SARS-CoV-2 virus has led to a worldwide crisis. In view of emerging variants time to time, there is a pressing need of effective COVID-19 therapeutics. Setomimycin, a rare tetrahydroanthracene antibiotic, remained unexplored for its therapeutic uses. Herein, we report our investigations on the potential of setomimycin as COVID-19 therapeutic. Pure setomimycin was isolated from Streptomyces sp. strain RA-WS2 from NW Himalayan region followed by establishing in silico as well as in vitro anti-SARS-CoV-2 property of the compound against SARS-CoV-2 main protease (Mpro). It was found that the compound targets Mpro enzyme with an IC50 value of 12.02 ± 0.046 μM. The molecular docking study revealed that the compound targets Glu166 residue of Mpro enzyme, hence preventing dimerization of SARS-CoV-2 Mpro monomer. Additionally, the compound also exhibited anti-inflammatory and anti-oxidant property, suggesting that setomimycin may be a viable option for application against COVID-19 infections. Graphical abstract ![]()
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Affiliation(s)
- Ravi S Manhas
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Harshita Tiwari
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Mateen Noor
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Ajaz Ahmed
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Jyoti Vishwakarma
- Division of Biochemistry and Structural Biology, CSIR- Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Raja B M Tripathi
- Division of Biochemistry and Structural Biology, CSIR- Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Ravishankar Ramachandran
- Division of Biochemistry and Structural Biology, CSIR- Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Sreedhar Madishetti
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Debaraj Mukherjee
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India
| | - Amit Nargotra
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India.
| | - Asha Chaubey
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
- Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad, 201002, India.
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