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Sivadas S, Mohanty AK, Rajesh S, Muthuvel SK, Vasanthi HR. Molecular modelling and biological evaluation of phyto-molecules as potential activators of gluconolactone oxidase (GULO). J Biomol Struct Dyn 2023; 41:15124-15136. [PMID: 36883880 DOI: 10.1080/07391102.2023.2187227] [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: 09/13/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Diabetes, the cause of colossal economic and disease burden, is a key area of research in drug discovery programs. Elevated blood glucose levels in diabetes lead to several adverse consequences due to the formation of advanced glycation end products and free radicals. Vitamin C, a potent antioxidant, protects the body's cells and tissues from oxidative damage and dysfunctions. Glucose is the precursor of Vitamin C synthesis in plants and some mammals. L-gulono lactone oxidase (GULO) is the rate-limiting enzyme in producing Vitamin C. However, it is not synthesized in bats, primates, humans, and guinea pigs because of the pseudogene. Several phytomolecules having antioxidant properties are hypothesized to be promising and selective activators of GULO. Therefore, the present study focused on screening agonists of GULO from phytomolecules as an effective augmentor for Vitamin C synthesis, thereby suppressing the sequela of diabetic events. The 3D structure of GULO was generated by the ab-initio method. Subsequently, molecular docking explored the possible binding patterns of GULO protein with different plant phenolic compounds, followed by supplementation of the potent phytomolecules to diabetic guinea pigs. It is noteworthy that Resveratrol and Hydroxytyrosol showed better binding affinity. The molecular simulation also confirmed that Resveratrol is an activator of the GULO enzyme. Interestingly, it was also established that Vitamin C levels were improved in diabetic guinea pigs supplemented with the phytomolecules and comparatively Resveratrol modulates the concentration of glucose and Vitamin C levels substantially, thereby alleviating hyperglycemia. However, further studies are warranted to study the mechanisms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sneha Sivadas
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Amaresh Kumar Mohanty
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Saranga Rajesh
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Suresh Kumar Muthuvel
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Hannah R Vasanthi
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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Ngaini Z, Rasin F, Wan Zullkiplee WSH, Abd Halim AN. Synthesis and molecular design of mono aspirinate thiourea-azo hybrid molecules as potential antibacterial agents. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2020.1828885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zainab Ngaini
- Faculty of Resource Science and Technology, Kota Samarahan, Malaysia
| | - Ferlicia Rasin
- Faculty of Resource Science and Technology, Kota Samarahan, Malaysia
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Vudhya Gowrisankar Y, Manne Mudhu S, Pasupuleti SK, Suthi S, Chaudhury A, Sarma PVGK. Staphylococcus aureus grown in anaerobic conditions exhibits elevated glutamine biosynthesis and biofilm units. Can J Microbiol 2020; 67:323-331. [PMID: 33136443 DOI: 10.1139/cjm-2020-0434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The enormous spread of Staphylococcus aureus infections through biofilms is a major concern in hospital-acquired infections. Biofilm formation by S. aureus on any surface is facilitated by adjusting its redox status. This organism is a facultative anaerobe shift more towards reductive conditions by enhancing nitrogen metabolism where glutamine synthesis plays a key role. Glutamine is synthesized by glutamine synthetase (GS) encoded by the glnA gene. The gene was amplified by PCR from the chromosomal DNA of S. aureus, sequenced (HQ329146.1), and cloned. The pure recombinant GS exhibited Km of 11.06 ± 0.05 mmol·L-1 for glutamate and 2.4 ± 0.03 mmol·L-1 for ATP. The glnA gene sequence showed a high degree of variability with its human counterpart, while it was highly conserved in bacteria. Structural analysis revealed that the GS structure of S. aureus showed close homology with other Gram-positive bacteria and exhibited a high degree of variation with Escherichia coli GS. In the present study, we observed the increased presence of GS activity in multidrug-resistant strains of S. aureus with elevated biofilm units, grown in brain heart infusion broth; among them methicillin-resistant strains S. aureus LMV 3, 4, and 5 showed higher biofilm units. All these results explain the important role of glutamine biosynthesis with elevated biofilm units in the pathogenesis of S. aureus.
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Affiliation(s)
- Yugandhar Vudhya Gowrisankar
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India.,Department of Cosmeceutics, College of Pharmacy, China Medical University, Taichung 40402, Taiwan (Republic of China)
| | - Sunitha Manne Mudhu
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India
| | - Santhosh Kumar Pasupuleti
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Indianapolis, IN 46202, USA
| | - Subbarayudu Suthi
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India
| | - Abhijit Chaudhury
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India
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Nogara PA, Orian L, Rocha JBT. The Se …S/N interactions as a possible mechanism of δ-aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: A computational study. ACTA ACUST UNITED AC 2020; 15:100127. [PMID: 32572387 PMCID: PMC7280828 DOI: 10.1016/j.comtox.2020.100127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 01/26/2023]
Abstract
DPDS and PSA interacts with cysteine residues from AlaD active site. The Se…S interactions could be involved in the δ-AlaD inhibition. δ-AlaD from Cucumis sativus does not present cysteine residues in the active site. Se…N interactions could be involved in the organoselenium action.
Organoselenium compounds present many pharmacological properties and are promising drugs. However, toxicological effects associated with inhibition of thiol-containing enzymes, such as the δ-aminolevulinic acid dehydratase (δ-AlaD), have been described. The molecular mechanism(s) by which they inhibit thiol-containing enzymes at the atomic level, is still not well known. The use of computational methods to understand the physical–chemical properties and biological activity of chemicals is essential to the rational design of new drugs. In this work, we propose an in silico study to understand the δ-AlaD inhibition mechanism by diphenyl diselenide (DPDS) and its putative metabolite, phenylseleninic acid (PSA), using δ-AlaD enzymes from Homo sapiens (Hsδ-AlaD), Drosophila melanogaster (Dmδ-AlaD) and Cucumis sativus (Csδ-AlaD). Protein modeling homology, molecular docking, and DFT calculations are combined in this study. According to the molecular docking, DPDS and PSA might bind in the Hsδ-AlaD and Dmδ-AlaD active sites interacting with the cysteine residues by Se…S interactions. On the other hand, the DPDS does not access the active site of the Csδ-AlaD (a non-thiol protein), while the PSA interacts with the amino acids residues from the active site, such as the Lys291. These interactions might lead to the formation of a covalent bond, and consequently, to the enzyme inhibition. In fact, DFT calculations (mPW1PW91/def2TZVP) demonstrated that the selenylamide bond formation is energetically favored. The in silico data showed here are in accordance with previous experimental studies, and help us to understand the reactivity and biological activity of organoselenium compounds.
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Affiliation(s)
- Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
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Novel mutations in the kinase domain of BCR-ABL gene causing imatinib resistance in chronic myeloid leukemia patients. Sci Rep 2019; 9:2412. [PMID: 30787317 PMCID: PMC6382822 DOI: 10.1038/s41598-019-38672-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/14/2018] [Indexed: 01/16/2023] Open
Abstract
Mutations in the drug binding region of BCR-ABL lead to imatinib resistance during the management of chronic myeloid leukemia (CML). In our study, 62 Philadelphia positive (Ph+) CML patients showing conspicuous expression of BCR-ABL gene were treated with imatinib. At the end of 3 months, 21/62 (33.87%) patients did not obtain complete hematological response (CHR) and also showed no significant decrease in BCR-ABL gene expression. In all the imatinib-resistant patients BCR-ABL gene was PCR amplified and sequenced. The sequence analysis showed four novel missense mutations p.(Leu301Ile), p.(Tyr320His), p.(Glu373Asp), p.(Asp381Asn) and six already reported mutations p.(Val256Gly), p.(Thr315Ile), p.(Gly250Glu), p.(Tyr253His), p.(Phe317Leu), p.(Met351Thr) which contributed in the formation of inactive enzyme and also two novel frameshift mutations p.(Glu281*) and p.(Tyr393*), which resulted in truncated protein formation. Further, the structural analysis revealed all these mutations affected P-loop, gatekeeper, catalytic and activation loop domain regions of the enzyme causing poor imatinib binding in the ATP region. The primary intention of the study was to find out the mutations in the BCR-ABL gene causing imatinib resistance. This study highlights the need for BCR-ABL gene sequence analysis to detect the mutations in CML patients in order to properly guide the therapy.
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Prasad UV, Vasu D, Gowtham RR, Pradeep CK, Swarupa V, Yeswanth S, Choudhary A, Sarma PVGK. Cloning, Expression and Characterization of NAD Kinase from Staphylococcus aureus Involved in the Formation of NADP (H): A Key Molecule in the Maintaining of Redox Status and Biofilm Formation. Adv Biomed Res 2017; 6:97. [PMID: 28828348 PMCID: PMC5549544 DOI: 10.4103/2277-9175.211833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Staphylococcus aureus has the ability to form biofilms on any niches, a key pathogenic factor of this organism and this phenomenon is directly related to the concentration of NADPH. The formation of NADP is catalyzed by NAD kinase (NADK) and this gene of S. aureus ATCC 12600 was cloned, sequenced, expressed and characterized. MATERIALS AND METHODS The NADK gene was polymerase chain reaction amplified from the chromosomal DNA of S. aureus ATCC 12600 and cloned in pQE 30 vector, sequenced and expressed in Escherichia coli DH5α. The pure protein was obtained by passing through nickel metal chelate agarose column. The enzyme kinetics of the enzyme and biofilm assay of the S. aureus was carried out in both aerobic and anaerobic conditions. The kinetics was further confirmed by the ability of the substrates to dock to the NADK structure. RESULTS The recombinant NADK exhibited single band with a molecular weight of 31kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the gene sequence (GenBank: JN645814) revealed presence of only one kind of NADK in all S. aureus strains. The enzyme exhibited very high affinity for NAD compared to adenosine triphosphate concurring with the docking results. A root-mean-square deviation value 14.039Å observed when NADK structure was superimposed with its human counterpart suggesting very low homology. In anaerobic conditions, higher biofilm units were found with decreased NADK activity. CONCLUSION The results of this study suggest increased NADPH concentration in S. aureus plays a vital role in the biofilm formation and survival of this pathogen in any environmental conditions.
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Affiliation(s)
- U Venkateswara Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - D Vasu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - R Rishi Gowtham
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Ch Krishna Pradeep
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - V Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - S Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Abhijit Choudhary
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - P V G K Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
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Vasu D, Sunitha MM, Srikanth L, Swarupa V, Prasad UV, Sireesha K, Yeswanth S, Kumar PS, Venkatesh K, Chaudhary A, Sarma PVGK. In Staphylococcus aureus the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation. 3 Biotech 2015; 5:505-512. [PMID: 28324552 PMCID: PMC4522715 DOI: 10.1007/s13205-014-0248-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022] Open
Abstract
Staphylococcus aureus, a natural
inhabitant of nasopharyngeal tract, survives mainly as biofilms. Previously we have observed that S. aureus ATCC 12600 grown under anaerobic conditions exhibited high rate of biofilm formation and l-lactate dehydrogenase activity. Thus, the concentration of pyruvate plays a critical role in S. aureus, which is primarily catalyzed by pyruvate kinase (PK). Analyses of the PK gene sequence (JN645815) revealed presence of PknB site in PK gene indicating that phosphorylation may be influencing the functioning of PK. To establish this hypothesis the pure enzymes of S. aureus ATCC 12600 were obtained by expressing these genes in PK 1 and PV 1 (JN695616) clones and passing the cytosolic fractions through nickel metal chelate column. The molecular weights of pure recombinant PK and PknB are 63 and 73 kDa, respectively. The enzyme kinetics of pure PK showed KM of 0.69 ± 0.02 µM, while the KM of PknB for stpks (stpks = NLCNIPCSALLSSDITASVNCAK) substrate was 0.720 ± 0.08 mM and 0.380 ± 0.07 mM for autophosphorylation. The phosphorylated PK exhibited 40 % reduced activity (PK = 0.2 ± 0.015 μM NADH/min/ml to P-PK = 0.12 ± 0.01 μM NADH/min/ml). Elevated synthesis of pyruvate kinase was observed in S. aureus ATCC 12600 grown in anaerobic conditions suggesting that the formed pyruvate is more utilized in the synthesis phase, supporting increased rate of biofilm formation.
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Affiliation(s)
- D Vasu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - M M Sunitha
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - L Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - V Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - U Venkateswara Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - K Sireesha
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - S Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - P Santhosh Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - K Venkatesh
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - Abhijit Chaudhary
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - P V G K Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India.
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Kumar PS, Kumar YN, Prasad UV, Yeswanth S, Swarupa V, Vasu D, Venkatesh K, Srikanth L, Rao VK, Sarma PVGK. Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases. Indian J Pharm Sci 2014; 76:430-6. [PMID: 25425757 PMCID: PMC4243260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/16/2022] Open
Abstract
Glucokinase is classified in bacteria based upon having ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif, the sequence of glucokinase gene (JN645812) of Staphylococcus aureus ATCC12600 showed presence of ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif. We have earlier observed glucokinase of S. aureus has higher affinity towards the substrate compared to other bacterial glucokinase and under anaerobic condition with increased glucose concentration S. aureus exhibited higher rate of biofilm formation. To establish this, 3D structure of glucokinase was built using homology modeling method, the PROCHECK and ProSA-Web analysis indicated this built glucokinase structure was close to the crystal structure. This structure was superimposed with different bacterial glucokinase structures and from the root-mean-square deviation values, it is concluded that S. aureus glucokinase exhibited very close homology with Enterococcus faecalis and Clostridium difficle while with other bacteria it showed high degree of variations both in domain and nondomain regions. Glucose docking results indicated -12.3697 kcal/mol for S. aureus glucokinase compared with other bacterial glucokinase suggesting higher affinity of glucose which correlates with enzyme kinetics and higher rate of biofilm formation.
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Affiliation(s)
- P. S. Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - Y. N. Kumar
- Department of Zoology, Sri Venkateswara University, Tirupati-517 502, India
| | - U. V. Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - S. Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - V. Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - D. Vasu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - K. Venkatesh
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - L. Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - V. K. Rao
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66047, USA
| | - P. V. G. K. Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
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