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Batjargal A, Solek P, Kukula-Koch W, Urjin B, Koch W, Koman D, Dudzinska E. Gurgem-7 toxicity assessment: Regulation of cell survival or death by traditional Mongolian prescription. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113660. [PMID: 35605329 DOI: 10.1016/j.ecoenv.2022.113660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/09/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Surgical treatments and chemotherapy are the most commonly used methods of colorectal cancer treatment (CRC), unfortunately, these therapies have many side effects. Moreover, despite advances in primary and adjuvant treatments, the survival time in CRC patients is still unsatisfactory. Treatment options for patients with CRC continue to advance and recent research has shown that colorectal cancer is sensitive to plant-derived substances. The use of natural compounds contained in herbal extracts for the treatment of colon cancer or as adjunctive therapy for CRC gives patients a wide range of treatment options. In this study, we evaluate the potential toxicity of the Mongolian preparation - Gurgem-7 composed of Crocus sativus, Veronica officinalis, Capsella bursa-pastoris, Arctostaphylos uva-ursi, Calendula officinalis, Gentiana lutea, and Terminalia chebula. Therefore, the aim of this study was to determine its biological activities, biochemical and molecular features in vitro and composition analysis by HPLC-ESI-QTOF-MS/MS platform. We identified 18 metabolites and 8 of them were quantified. Majority of the secondary metabolites belonged to the group of phenolic constituents with taxifolin, chlorogenic acids' family, hydroxysafflor yellow A and hydroxybenzoic acid as leading compounds. In turn, our in vitro results suggest that the preparation inhibits cell metabolic activity through oxidative stress, numerous DNA damage and cell cycle arrest. Simultaneously enzymatic and non-enzymatic cell protection mechanisms mediated by TP53/Keap1 and Nrf2/HO-1 pathways may be activated in a cell-specific manner in vitro. In conclusion, we provide preliminary molecular evidence of the toxic properties of Gurgem-7 preparation to Caco-2 and CT26. WT cells related to insufficient action of their repair and adaptive mechanisms to stress conditions.
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Affiliation(s)
- Ariunzaya Batjargal
- Mon-Intra CO., LTD, 23 sh/h 166 Mongolian, Ulaanbaatar, Mongolia; Department of Food and Nutrition, Medical University of Lublin, 20-093 Lublin, Poland
| | - Przemyslaw Solek
- Department of Biopharmacy, Medical University of Lublin, Lublin 20-093, Poland; Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszow, Rzeszow 35-310, Poland
| | - Wirginia Kukula-Koch
- Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Lublin, 20-093 Lublin, Poland
| | - Baigalmaa Urjin
- Mon-Intra CO., LTD, 23 sh/h 166 Mongolian, Ulaanbaatar, Mongolia
| | - Wojciech Koch
- Department of Food and Nutrition, Medical University of Lublin, 20-093 Lublin, Poland
| | - Dorota Koman
- Mon-Intra CO., LTD, 23 sh/h 166 Mongolian, Ulaanbaatar, Mongolia
| | - Ewa Dudzinska
- Department of Food and Nutrition, Medical University of Lublin, 20-093 Lublin, Poland.
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Agarwal V, Yadav TC, Tiwari A, Varadwaj PK. Insights into structure and activity relationship of clinically mutated PER1 and PER2 class A β-lactamase enzymes. J Biomol Struct Dyn 2022:1-18. [PMID: 35475497 DOI: 10.1080/07391102.2022.2066179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
PER1 and PER2 are among the class A β-lactamase enzymes, which have evolved clinically to form antibiotic resistance and have significantly expanded their spectrum of activity. Hence, there is a need to study the clinical mutation responsible for such β-lactamase mediated antibiotic resistance. Alterations in catalytic centre and Ω-loop structure could be the cause of antibiotic resistance in these β-lactamase enzymes. Structural and functional alterations are caused due to mutations on or near the catalytic centre, which results in active site plasticity and are responsible for its expanded spectrum of activity in these class A β-lactamase enzymes. Multiple sequence alignment, structure, kinetic, molecular docking, MMGBSA and molecular dynamic simulation comparisons were done on 38 clinically mutated and wild class A β-lactamase enzymes. This work shows that PER1 and PER2 enzymes contains most unique mutations and have altered Ω-loop structure, which could be responsible for altering the structure-activity relationship and extending the spectrum of activity of these enzymes. Alterations in molecular docking, MMGBSA, kinetic values reveals the modification in the binding and activity of these clinically mutated enzymes with antibiotics. Further, the cause of these alterations can be revealed by active site interactions and H-bonding pattern of these enzymes with antibiotics. Met69Gln, Glu104Thr, Tyr105Trp, Met129His, Pro167Ala, Glu168Gln, Asn170His, Ile173Asp and Asp176Gln mutations were uniquely found in PER1 and PER2 enzymes. These mutations occurs at catalytic important residues and results in altered interactions with β-lactam antibiotics. Hence, these mutations could be responsible for altering the structure-activity of PER1 and PER2 enzymes.
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Affiliation(s)
- Vidhu Agarwal
- Department of Applied Sciences, Indian Institute of Information Technology, Jhalwa, Allahabad, India
| | - Tara Chand Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, India
| | - Akhilesh Tiwari
- Department of Applied Sciences, Indian Institute of Information Technology, Jhalwa, Allahabad, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Jhalwa, Allahabad, India
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Ardalan N, Akhavan Sepahi A, Khavari-Nejad RA. Development of Escherichia coli asparaginase II for the Treatment of Acute Lymphocytic Leukemia: In Silico Reduction of asparaginase II Side Effects by a Novel Mutant (V27F). Asian Pac J Cancer Prev 2021; 22:1137-1147. [PMID: 33906306 PMCID: PMC8325130 DOI: 10.31557/apjcp.2021.22.4.1137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/31/2021] [Indexed: 12/02/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a common blood disease in children that is accountable for many deaths. Due to major improvements in treatment procedures in the past 50 years, the survivability of this disease has risen dramatically to about 90 percent today. L-asparaginase (ASNase) has been used to treat ALL. The glutaminase (GLNase) activity of this enzyme causes some side effects and is unnecessary for anticancer activity. This study investigated mutagenesis in Escherichia coli ASNase II to find a mutant with lower GLNase activity via molecular dynamics (MD) simulation. Residues with low binding energy to asparagine (Asn) and high binding energy to glutamine (Gln) were chosen for mutagenesis. A mutant with low free binding energy to Gln was then selected for molecular docking and MD studies. The results showed that V27F is a good candidate for reducing GLNase activity and that it has little effect on enzyme ASNase activity. A simulation analysis showed that the V27F mutant was more stable than the WT ASNase and that mutagenesis was quite successful.
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Affiliation(s)
- Noeman Ardalan
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Abbas Akhavan Sepahi
- Department of Microbiology, Faculty of Science, North Branch, Islamic Azad University, Tehran, Iran.
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Aghaeepoor M, Akbarzadeh A, Mirzaie S, Hadian A, Jamshidi Aval S, Dehnavi E. Selective reduction in glutaminase activity of l‑Asparaginase by asparagine 248 to serine mutation: A combined computational and experimental effort in blood cancer treatment. Int J Biol Macromol 2018; 120:2448-2457. [DOI: 10.1016/j.ijbiomac.2018.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/02/2018] [Accepted: 09/04/2018] [Indexed: 01/16/2023]
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5
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Davari K, Nowroozi J, Hosseini F, Sepahy AA, Mirzaie S. Structure-based virtual screening to identify the beta-lactamase CTX-M-9 inhibitors: An in silico effort to overcome antibiotic resistance in E. coli. Comput Biol Chem 2017; 67:174-181. [DOI: 10.1016/j.compbiolchem.2017.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/05/2017] [Accepted: 01/18/2017] [Indexed: 11/26/2022]
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Structure-based virtual screening efforts against HIV-1 reverse transcriptase to introduce the new potent non-nucleoside reverse transcriptase inhibitor. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.07.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Rani N, Vijayakumar S, P T V L, Arunachalam A. Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination. J Biomol Struct Dyn 2016; 34:1778-96. [PMID: 26360629 DOI: 10.1080/07391102.2015.1092096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.
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Affiliation(s)
- Nidhi Rani
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , R. V. Nagar Kalapet, Pondicherry 605014 , India
| | - Saravanan Vijayakumar
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , R. V. Nagar Kalapet, Pondicherry 605014 , India.,b Centre for Advanced Study in Crystallography and Biophysics , University of Madras , Tamilnadu , India
| | - Lakshmi P T V
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , R. V. Nagar Kalapet, Pondicherry 605014 , India
| | - Annamalai Arunachalam
- c Department of Botany , Sethupathy Government Arts and Science College, Alagappa University , Ramanathpuram , Tamil Nadu , India
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Wang YT, Cheng TL. Refined models of New Delhi metallo-beta-lactamase-1 with inhibitors: an QM/MM modeling study. J Biomol Struct Dyn 2016; 34:2214-23. [DOI: 10.1080/07391102.2015.1110834] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yeng-Tseng Wang
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, Kaohsiung 80708, Taiwan, P.R. China
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan, P.R. China
| | - Tian-Lu Cheng
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan, P.R. China
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Rehman MT, Ahmed S, Khan AU. Interaction of meropenem with ‘N’ and ‘B’ isoforms of human serum albumin: a spectroscopic and molecular docking study. J Biomol Struct Dyn 2015; 34:1849-64. [DOI: 10.1080/07391102.2015.1094411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Md. Tabish Rehman
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202 002, India
| | - Sarfraz Ahmed
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202 002, India
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202 002, India
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Mollica A, Mirzaie S, Costante R, Carradori S, Macedonio G, Stefanucci A, Dvoracsko S, Novellino E. Exploring the biological consequences of conformational changes in aspartame models containing constrained analogues of phenylalanine. J Enzyme Inhib Med Chem 2015; 31:953-63. [PMID: 26308194 DOI: 10.3109/14756366.2015.1076811] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The dipeptide aspartame (Asp-Phe-OMe) is a sweetener widely used in replacement of sucrose by food industry. 2',6'-Dimethyltyrosine (DMT) and 2',6'-dimethylphenylalanine (DMP) are two synthetic phenylalanine-constrained analogues, with a limited freedom in χ-space due to the presence of methyl groups in position 2',6' of the aromatic ring. These residues have shown to increase the activity of opioid peptides, such as endomorphins improving the binding to the opioid receptors. In this work, DMT and DMP have been synthesized following a diketopiperazine-mediated route and the corresponding aspartame derivatives (Asp-DMT-OMe and Asp-DMP-OMe) have been evaluated in vivo and in silico for their activity as synthetic sweeteners.
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Affiliation(s)
- Adriano Mollica
- a Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio" , Chieti , Italy
| | - Sako Mirzaie
- b Department of Biochemistry, Sanandaj Branch , Islamic Azad University , Sanandaj , Iran
| | - Roberto Costante
- a Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio" , Chieti , Italy
| | - Simone Carradori
- a Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio" , Chieti , Italy
| | - Giorgia Macedonio
- a Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio" , Chieti , Italy
| | | | - Szabolcs Dvoracsko
- d Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences , Temesvari krt , Hungary , and
| | - Ettore Novellino
- e Dipartimento di Farmacia, Università di Napoli "Federico II" , Naples , Italy
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Shahverdi AR, Mirzaie S, Rafii F, Kakavand M, Foroumadi A. Monoterpenes as nitrofurantoin resistance modulating agents: minimal structural requirements, molecular dynamics simulations, and the effect of piperitone on the emergence of nitrofurantoin resistance in Enterobacteriaceae. J Mol Model 2015; 21:198. [PMID: 26174760 DOI: 10.1007/s00894-015-2741-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/24/2015] [Indexed: 01/10/2023]
Abstract
The effects of different monoterpenes and 2-cyclohexen-1-one on the antibacterial activity of nitrofurantoin against resistant Enterobacter cloacae, were compared and the minimal structural component of monoterpene required for the highest level of resistance-modulating activity was determined. Subinhibitory concentrations of all compounds tested enhanced the antibacterial activity of nitrofurantoin against E. cloacae to different extents. The highest synergistic effect was observed for the monoterpenes, like piperitone, which contained a conjugated ketone and C=C bond in their carbon ring structure. Piperitone also suppressed the emergence of nitrofurantoin-resistant strains of Enterobacteriaceae that were mutagenized by ethyl methanesulfonate. The modes of interaction of carvone, piperitone, and an enzyme inhibitor, benzoate, with nitroreductase were investigated by molecular docking and molecular dynamic (MD) simulation for 20 ns. MD simulation supported greater stability of the benzoate and monoterpene-nitroreductase (NR) complexes than of free NR. The results of this investigation are promising for the synthesis of more effective lead compounds to enhance the antibacterial activity of nitro drugs against resistant Enterobacter strains.
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Affiliation(s)
- Ahmad R Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, 1417614411, Iran,
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