1
|
Devi AM, Sankeshi V, Ravali A, Bandaru S, Theendra VK, Sagurthi SR. Inhibitory effect of Nifedipine on aldose reductase delays cataract progression. Naunyn Schmiedebergs Arch Pharmacol 2024; 397:161-171. [PMID: 37395794 DOI: 10.1007/s00210-023-02588-1] [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] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023]
Abstract
Aldose reductase (ALR2) is a rate-limiting component of the polyol pathway, which is essential for the NADPH-mediated conversion from glucose to sorbitol. ALR2 dysregulation has been linked to α-crystallin aggregation, increased oxidative stress, and calcium inflow, all of which contribute to a diabetic cataract. Given its crucial role in occular pathologies, ALR2 has emerged as a promising target to treat oxidative stress and hyperglycaemic condition which form the underlying cause of diabetic cataracts. However, several of them had issues with sensitivity and specificity to ALR2, despite being screened as effective ALR2 inhibitors from a wide range of structurally varied molecules. The current study investigates the inhibitory potential of Nifedipine, an analog of the dihydro nicotinamide class of compounds against ALR2 activity. The enzyme inhibition studies were supported by in vitro biomolecular interactions, molecular modeling approaches, and in vivo validation in diabetic rat models. Nifedipine demonstrated appreciable inhibitory potential with the purified recombinant hAR (human aldose reductase; with an IC50 value of 2.5 µM), which was further supported by Nifedipine-hAR binding affinity (Kd = 2.91 ± 1.87 × 10-4 M) by ITC and fluorescence quenching assays. In the in vivo models of STZ-induced diabetic rats, Nifedipine delayed the onset progression of cataracts by preserving the antioxidant enzyme activity (SOD, CAT, and GPX GSH, TBARS, and protein carbonyls) and was shown to retain the α-crystallin chaperone activity by reducing the calcium levels in the diabetic rat lens. In conclusion, our results demonstrate effective inhibition of ALR2 by Nifedipine, resulting in amelioration of diabetic cataract conditions by lowering oxidative and osmotic stress while retaining the chaperone activity of α-crystallins. The present study could be envisaged to improve the eye condition in older adults upon Nifedipine treatment.
Collapse
Affiliation(s)
- Alaparthi Malini Devi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, 500007, India
| | - Venu Sankeshi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, 500007, India
| | - Arugonda Ravali
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, 500007, India
| | - Srinivas Bandaru
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation (Deemed to be University), Guntur, 522302, India
| | | | - Someswar Rao Sagurthi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, 500007, India.
| |
Collapse
|
2
|
Akkiraju AG, Badugu A, Das A, Sagurthi SR. Molecular docking-based screening of methicillin-resistant Staphylococcus aureus FEM proteins with FDA-approved drugs. Bioinformation 2023; 19:1035-1042. [PMID: 38046517 PMCID: PMC10692981 DOI: 10.6026/973206300191035] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023] Open
Abstract
Antibiotic resistance stands as one of the most significant public health challenges in recent decades. FEM proteins are responsible for the synthesis of pentaglycine cross-bridge, a primary constituent of bacterial peptidoglycan polymer crosslinking during cell wall biosynthesis. Since they are necessary for bacterial survival and antibiotic resistance, they were considered as significant antibacterial targets. We report herein, the virtual screening and selection of FDA-approved drugs and their potent similar molecules as FEM protein inhibitors and analyzed for inhibiting affinity and their ADMET pharmacokinetic properties. This data provide a foundation for the development and optimization of structurally innovative antimicrobial drugs.
Collapse
Affiliation(s)
- Anjini Gayatri Akkiraju
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Aishwaraya Badugu
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Aditi Das
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Someswar Rao Sagurthi
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| |
Collapse
|
3
|
Akkiraju AG, Atcha KR, Sagurthi SR. Cloning, Purification, and Biophysical Characterization of FemB Protein from Methicillin-Resistant Staphylococcus aureus and Inhibitors Screening. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04780-8. [PMID: 37991634 DOI: 10.1007/s12010-023-04780-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Methicillin-resistant Staphylococcus aureus has emerged as a leading cause of nosocomial, community acquired infections worldwide. Earlier investigations revealed that mecA-encoded FEM proteins play a role in antimicrobial resistance by developing unique peptidoglycan cross-linking which helps in the formation of protective cell membrane. In view to this, present study focused on expression, purification FEM proteins, and FemB biophysical characterization with the aid of in silico and in vitro approaches. Furthermore, we carried out biological screening assays and identified the novel potent 1,2,3-triazole conjugated 1,3,4-oxadiazole hybrid molecule which could inhibit the MRSA than the proven oxacillin.
Collapse
Affiliation(s)
- Anjini Gayatri Akkiraju
- Molecular Medicine Lab, Dept. of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Krishnam Raju Atcha
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana, 500001, India
| | - Someswar Rao Sagurthi
- Molecular Medicine Lab, Dept. of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
4
|
Kumari PS, Kumar DR, Charan GV, Sagurthi SR. Structural, photocatalytic, and anticancer activity Ni-substituted Cu nanochromites synthesized by citrate gel auto-combustion method. Chem Pap 2023. [DOI: 10.1007/s11696-023-02798-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
5
|
Barmukh R, Roorkiwal M, Dixit GP, Bajaj P, Kholova J, Smith MR, Chitikineni A, Bharadwaj C, Sreeman SM, Rathore A, Tripathi S, Yasin M, Vijayakumar AG, Rao Sagurthi S, Siddique KHM, Varshney RK. Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. J Exp Bot 2022; 73:7255-7272. [PMID: 36006832 PMCID: PMC9730794 DOI: 10.1093/jxb/erac348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 05/16/2023]
Abstract
'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.
Collapse
Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Girish P Dixit
- ICAR - Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jana Kholova
- Crops Physiology & Modeling, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
| | - Millicent R Smith
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Australia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Chellapilla Bharadwaj
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- ICAR - Indian Agricultural Research Institute (IARI), Delhi, India
| | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Abhishek Rathore
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Mohammad Yasin
- RAK College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | | |
Collapse
|
6
|
Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. Plant Biotechnol J 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
Collapse
Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| |
Collapse
|
7
|
Peddada LM, Sagurthi SR, Guguloth VC, Annapragada R, Kanuparthy PR. Visible Light Driven Photodegradation of Pathological Effluents and Biological Evaluation of Green ZnO Nanoparticles. ChemistrySelect 2022. [DOI: 10.1002/slct.202200146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lakshmi Madhuri Peddada
- School of Science GITAM (Deemed to be University) Hyderabad Telangana 502329 India
- St. Francis College for Women, Begumpet Hyderabad Telangana 500016 India
| | - Someswar Rao Sagurthi
- Department of Genetics and Biotechnology University College of Science Osmania University Hyderabad Telangana 500007 India
| | - Vijaya Charan Guguloth
- Department of Chemistry University College of Science Osmania University Hyderabad Telangana 500007 India
| | | | | |
Collapse
|
8
|
Md. Jasmine SK, Reddy G. VS, Gorityala N, Sagurthi SR, Mungapati S, Manikanta KN, Allam US. In Silico Modeling and Docking Analysis of CTX-M-5, Cefotaxime-Hydrolyzing β-Lactamase from Human-Associated Salmonella Typhimurium. J Pharmacol Pharmacother 2022. [DOI: 10.1177/0976500x221109721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background: CTX-M-type enzymes represent a novel and rapidly evolving group of extended-spectrum β-lactamases, which confer resistance to advance generation cephalosporins. Despite the interaction of CTX-M-5 with drugs and inhibitors, its structure is not reported till date. The present study aimed to computationally model the CTX-M-5 β-lactamase and establish its structure, which is exclusively present in human-associated Salmonella. Methods: The CTX-M-5 aminoacid sequence (Uniprot ID:O65975) of Salmonella enterica subsp. enterica serovar typhimurium was retrieved from UniProt database and subjected to homology modeling using MODELLER 9v7. The homology models were duly validated using RAMPAGE tool by generating Ramachandran plots, ERRAT graphs, and ProSA score. DoGSiteScorer server and ConSurf server were used to detect the cavities, pockets, and clefts to identify conserved amino acid sites in the predicted model. Subsequently, the modeled structure was docked using CLC Drug Discovery Workbench against proven drugs and known inhibitors. Results: Obtained high-quality homology model with 91.7% of the residues in favorable regions in Ramachandran plot and qualified in other quality parameters. Docking studies resulted in a higher dock score for PNK (D-benzylpenicilloic acid) molecule when compared to other reported inhibitors. Conclusion: This in silico study suggests that the compound PNK could be an efficient ligand for CTX-M-5 β-lactamase and serve as a potent inhibitor of CTX-M-5.
Collapse
Affiliation(s)
- S. K. Md. Jasmine
- Department of Biotechnology, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India
| | - Vidya Sagar Reddy G.
- Department of Biotechnology, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India
| | - Neelima Gorityala
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar Rao Sagurthi
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Sandhya Mungapati
- Department of Crop Production, DAATTC Center, Acharya N G Ranga Agricultural University, Nellore, Andhra Pradesh, India
| | - Kota Neela Manikanta
- Department of Travel and Tourism, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India
| | - Uday Sankar Allam
- Department of Biotechnology, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India
| |
Collapse
|
9
|
Bitla S, Gayatri AA, Puchakayala MR, Kumar Bhukya V, Vannada J, Dhanavath R, Kuthati B, Kothula D, Sagurthi SR, Atcha KR. Design and synthesis, biological evaluation of bis-(1,2,3- and 1,2,4)-triazole derivatives as potential antimicrobial and antifungal agents. Bioorg Med Chem Lett 2021; 41:128004. [PMID: 33811989 DOI: 10.1016/j.bmcl.2021.128004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 01/23/2021] [Revised: 03/13/2021] [Accepted: 03/25/2021] [Indexed: 11/27/2022]
Abstract
A new series of bis-1,2,3- and 1,2,4-triazoles (10a-m) were designed and efficiently synthesized using methyl salicylate as potential antimicrobial agents. All compounds were characterized by their proton & 13C NMR, IR, Mass spectral data, and elemental analysis. The final compounds 10a-m were in vitro screened for antimicrobial and antifungal activity against gram negative Pseudomonas aeruginosa, Escherichia coli, gram positive Bacillus subtilis, Staphylococcus aureus strains and Aspergillus niger & Saccharomyces cerevisiae. Majority of the synthesized compounds exhibited potent antimicrobial activity (MIC 3.9 µg/mL) and promising antifungal activity with the zone of inhibition (ZOI) 1.5-8.2 mm. Compounds like 10d and 10f exhibited best antimicrobial activity against S. aureus. The molecular docking analysis revealed that all the synthesized derivatives shown better binding affinities. Among all, compound 10f exhibited best scores. Hence, there was an assumption that introduction of para-chloro and bromo-phenyl aromatic groups on triazole moiety could result excellent antimicrobial activity. This substantial growth inhibitory activity of bis-1,2,3- and 1,2,4-triazole derivatives suggested these compounds could assist a new way in the development of lead molecules against microbial infection and antimicrobial resistance investigations.
Collapse
Affiliation(s)
- Sampath Bitla
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana 500001, India
| | - Akkiraju Anjini Gayatri
- Molecular Medicine Lab, Dept. of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana 500007, India
| | | | - Vijaya Kumar Bhukya
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana 500001, India
| | - Jagadeshwar Vannada
- Department of Chemistry, University College of Science, Saifabad, Osmania University, Hyderabad, Telangana 500004, India
| | - Ramulu Dhanavath
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana 500001, India
| | - Bhaskar Kuthati
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana 500007, India
| | - Devender Kothula
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana 500001, India
| | - Someswar Rao Sagurthi
- Molecular Medicine Lab, Dept. of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana 500007, India.
| | - Krisham Raju Atcha
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana 500001, India.
| |
Collapse
|
10
|
Nagamalla SS, Alaparthi MD, Mellacheruvu S, Gundeti R, Earrawandla JPS, Sagurthi SR. Morpho-Physiological and Proteomic Response of Bt-Cotton and Non-Bt Cotton to Drought Stress. Front Plant Sci 2021; 12:663576. [PMID: 34040622 PMCID: PMC8143030 DOI: 10.3389/fpls.2021.663576] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Drought stress impacts cotton plant growth and productivity across countries. Plants can initiate morphological, cellular, and proteomic changes to adapt to unfavorable conditions. However, our knowledge of how cotton plants respond to drought stress at the proteome level is limited. Herein, we elucidated the molecular coordination underlining the drought tolerance of two inbred cotton varieties, Bacillus thuringiensis-cotton [Bt-cotton + Cry1 Ac gene and Cry 2 Ab gene; NCS BG II BT (BTCS/BTDS)] and Hybrid cotton variety [Non-Bt-cotton; (HCS/HDS)]. Our morphological observations and biochemical experiments showed a different tolerance level between two inbred lines to drought stress. Our proteomic analysis using 2D-DIGE revealed that the changes among them were not obviously in respect to their controls apart from under drought stress, illustrating the differential expression of 509 and 337 proteins in BTDS and HDS compared to their controls. Among these, we identified eight sets of differentially expressed proteins (DEPs) and characterized them using MALDI-TOF/TOF mass spectrometry. Furthermore, the quantitative real-time PCR analysis was carried out with the identified drought-related proteins and confirmed differential expressions. In silico analysis of DEPs using Cytoscape network finds ATPB, NAT9, ERD, LEA, and EMB2001 to be functionally correlative to various drought-responsive genes LEA, AP2/ERF, WRKY, and NAC. These proteins play a vital role in transcriptomic regulation under stress conditions. The higher drought response in Bt cotton (BTCS/BTDS) attributed to the overexpression of photosynthetic proteins enhanced lipid metabolism, increased cellular detoxification and activation chaperones, and reduced synthesis of unwanted proteins. Thus, the Bt variety had enhanced photosynthesis, elevated water retention potential, balanced leaf stomata ultrastructure, and substantially increased antioxidant activity than the Non-Bt cotton. Our results may aid breeders and provide further insights into developing new drought-tolerant and high-yielding cotton hybrid varieties.
Collapse
|
11
|
Barmukh R, Roorkiwal M, Jaba J, Chitikineni A, Mishra SP, Sagurthi SR, Munghate R, Sharma HC, Varshney RK. Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.). Plant Genome 2020; 14:e20071. [PMID: 33289349 DOI: 10.1002/tpg2.20071] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/15/2020] [Indexed: 06/12/2023]
Abstract
Genetic enhancement for resistance against the pod borer, Helicoverpa armigera is crucial for enhancing production and productivity of chickpea. Here we provide some novel insights into the genetic architecture of natural variation in H. armigera resistance in chickpea, an important legume, which plays a major role in food and nutritional security. An interspecific recombinant inbred line (RIL) population developed from a cross between H. armigera susceptible accession ICC 4958 (Cicer arietinum) and resistant accession PI 489777 (Cicer reticulatum) was evaluated for H. armigera resistance component traits using detached leaf assay and under field conditions. A high-throughput AxiomCicerSNP array was utilized to construct a dense linkage map comprising of 3,873 loci and spanning a distance of 949.27 cM. Comprehensive analyses of extensive genotyping and phenotyping data identified nine main-effect QTLs and 955 epistatic QTLs explaining up to 42.49% and 38.05% phenotypic variance, respectively, for H. armigera resistance component traits. The main-effect QTLs identified in this RIL population were linked with previously described genes, known to modulate resistance against lepidopteran insects in crop plants. One QTL cluster harbouring main-effect QTLs for three H. armigera resistance component traits and explaining up to 42.49% of the phenotypic variance, was identified on CaLG03. This genomic region, after validation, may be useful to improve H. armigera resistance component traits in elite chickpea cultivars.
Collapse
Affiliation(s)
- Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jagdish Jaba
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Suraj Prasad Mishra
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajendra Munghate
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - H C Sharma
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| |
Collapse
|
12
|
Qureshi R, Alaparthi MD, Eligati PS, Hasan Razvi SR, Walvekar KP, Afraa M, Sagurthi SR. Molecular docking analysis of an isoflavone derivative with the protein phosphatase 1 from Leishmania donovani. Bioinformation 2020; 16:942-948. [PMID: 34803271 PMCID: PMC8573454 DOI: 10.6026/97320630016942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 09/21/2020] [Revised: 10/24/2020] [Accepted: 10/24/2020] [Indexed: 12/16/2022] Open
Abstract
Leishmaniasis is one of the most neglected diseases with high morbidity and mortality rate. Severe side effects with existing drug and lack of proper vaccine encouraged us to design alternative models to combat the disease. We showed that PP1 of Leishmania donovani mediates immunomodulation in host macrophages needed for parasite survival. Therefore, it is of interest to report the molecular docking analysis of 512 isoflavone derivatives with the phosphatase 1 protein from Leishmania donovani to highlight compound 362 (5-hydroxy-5-{9-[2-methoxy-2-(2-methylfuran-3-yl) ethyl]-1H, 3H, 4H, 10bH-pyrano[4,3-c]chromen-3-yl}pentanoic acid) having good binding features and acceptable ADMET properties for further consideration.
Collapse
Affiliation(s)
- Rahila Qureshi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| | - Malini Devi Alaparthi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| | - Prathyusha Sai Eligati
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| | - Syed Rizwan Hasan Razvi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| | - Komal Paresh Walvekar
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| | - Mohammad Afraa
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| | - Someswar Rao Sagurthi
- Drug Design & Molecular Medicine Laboratory, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana-500007, India
| |
Collapse
|
13
|
Bitla S, Sagurthi SR, Dhanavath R, Puchakayala MR, Birudaraju S, Gayatri AA, Bhukya VK, Atcha KR. Design and synthesis of triazole conjugated novel 2,5-diaryl substituted 1,3,4-oxadiazoles as potential antimicrobial and anti-fungal agents. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128705] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Sudhakar Mokenapelli, Gutam M, Yerrabelli JR, Irlapati VK, Gorityala N, Sagurthi SR, Chitneni PR. Design and Synthesis of Novel 2-Substituted-Benzyl-5-(2-Methylbenzofuran-3-yl)-2H-Tetrazoles: Anti-Proliferative Activity. Russ J Bioorg Chem 2020. [DOI: 10.1134/s1068162020050179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Sekhar T, Thriveni P, Ramesh K, Giri Prasad P, Srihari I, Gorityala N, Rao Sagurthi S, Sankar Allam U. Green synthesis, antitubercular evaluation, and molecular docking studies of ethyl 3,5-dicyano-6-oxo-2,4-diarylpiperidine-3-carboxylate derivatives. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02519-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
16
|
Ashok D, Madhuri EVL, Sarasija M, Sree Kanth S, Vijjulatha M, Gayatri AA, Sagurthi SR, Krishna NS. Synthesis of Biaryl Derivatives of Spirofurochromanone in Water and Their Anticancer Activity. RUSS J GEN CHEM+ 2019. [DOI: 10.1134/s1070363219100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Mokenapelli S, Gutam M, Vadiyaala N, Yerrabelli JR, Banerjee S, Roy P, Kancha RK, Kunduru BR, Sagurthi SR, Chitneni PR. Synthesis and cytotoxicity of novel 14α- O-(1,4-disubstituted-1,2,3-triazolyl) ester derivatives of andrographolide. Nat Prod Res 2019; 35:289-297. [PMID: 31219346 DOI: 10.1080/14786419.2019.1628746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A series of novel 14α-O-(1,4-disubstituted-1,2,3-triazolyl) ester derivatives of andrographolide (5a-n) were synthesized from andrographolide (1). For this endeavour, selective esterification at C-14 hydroxyl group of andrographolide (1) with propiolic acid via protection, deprotection strategy followed by 1,4-regioselective [1,3]dipolar cycloaddition of alkyne, azide using Cu(I) catalyzed Click chemistry. All the synthesized derivatives were screened for their cytotoxicity on HCT-15, HeLa and K562 cell lines. Compounds 5c and 5j showed highest activity against HCT-15 and K562 cell lines whereas compound 5a displayed activity in all the three cell lines. Loss of cell viability was not observed with the non-transformed cell line MRC-5 with compounds 5j, 5k, 5h and 2 indicating cytotoxic activity of these compounds towards cancer cell lines. Further, molecular docking analysis and SAR studies of highly active compounds 5c and 5j revealed enhanced binding affinity to the target NF-κB protein.
Collapse
Affiliation(s)
- Sudhakar Mokenapelli
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| | - Madhu Gutam
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| | - Naveen Vadiyaala
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| | | | - Somesh Banerjee
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Partha Roy
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Rama Krishna Kancha
- Molecular Medicine and Therapeutics Laboratory, Centre for Plant Molecular Biology, Osmania University, Hyderabad, Telangana, India
| | - Bharathi Reddy Kunduru
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar Rao Sagurthi
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Prasad Rao Chitneni
- Natural Products Laboratory, Department of Chemistry, Osmania University, Hyderabad, Telangana, India
| |
Collapse
|
18
|
Bangera M, Gowda K G, Sagurthi SR, Murthy MRN. Structural and functional insights into phosphomannose isomerase: the role of zinc and catalytic residues. Acta Crystallogr D Struct Biol 2019; 75:475-487. [PMID: 31063150 DOI: 10.1107/s2059798319004169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/28/2019] [Indexed: 11/10/2022]
Abstract
Phosphomannose isomerase (PMI) is a housekeeping enzyme that is found in organisms ranging from bacteria to fungi to mammals and is important for cell-wall synthesis, viability and signalling. PMI is a zinc-dependent enzyme that catalyses the reversible isomerization between mannose 6-phosphate (M6P) and fructose 6-phosphate (F6P), presumably via the formation of a cis-enediol intermediate. The reaction is hypothesized to involve ring opening of M6P, the transfer of a proton from the C2 atom to the C1 atom and between the O1 and O2 atoms of the substrate, followed by ring closure resulting in the product F6P. Several attempts have been made to decipher the role of zinc ions and various residues in the catalytic function of PMI. However, there is no consensus on the catalytic base and the mechanism of the reaction catalyzed by the enzyme. In the present study, based on the structure of PMI from Salmonella typhimurium, site-directed mutagenesis targeting residues close to the bound metal ion and activity studies on the mutants, zinc ions were shown to be crucial for substrate binding. These studies also suggest Lys86 as the most probable catalytic base abstracting the proton in the isomerization reaction. Plausible roles for the highly conserved residues Lys132 and Arg274 could also be discerned based on comparison of the crystal structures of wild-type and mutant PMIs. PMIs from prokaryotes possess a low sequence identity to the human enzyme, ranging between 30% and 40%. Since PMI is important for the virulence of many pathogenic organisms, the identification of catalytically important residues will facilitate its use as a potential antimicrobial drug target.
Collapse
Affiliation(s)
- Mamata Bangera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Giri Gowda K
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - S R Sagurthi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - M R N Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| |
Collapse
|
19
|
Shiva Raju K, AnkiReddy S, Sabitha G, Siva Krishna V, Sriram D, Bharathi Reddy K, Rao Sagurthi S. Synthesis and biological evaluation of 1H-pyrrolo[2,3-d]pyrimidine-1,2,3-triazole derivatives as novel anti-tubercular agents. Bioorg Med Chem Lett 2019; 29:284-290. [DOI: 10.1016/j.bmcl.2018.11.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/17/2018] [Indexed: 12/16/2022]
|
20
|
Jakkula P, Qureshi R, Iqbal A, Sagurthi SR, Qureshi IA. Leishmania donovani PP2C: Kinetics, structural attributes and in vitro immune response. Mol Biochem Parasitol 2018; 223:37-49. [PMID: 29964060 DOI: 10.1016/j.molbiopara.2018.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 02/28/2018] [Revised: 06/15/2018] [Accepted: 06/26/2018] [Indexed: 01/03/2023]
Abstract
Most of the signaling pathways are regulated by reversible phosphorylation-dephosphorylation which involves enzymes- kinases and phosphatases. Current knowledge about the protein phosphatases in parasites like Trypanosoma and Leishmania is very minimal despite their enormousity. In present study, full length ORF of Leishmania donovani PP2C was cloned into expression vector followed by purification and molecular weight determination using Ni-NTA affinity and gel giltration chromatography respectively. Purified LdPP2C was found to be enzymatically active, while inhibition study suggested that sanguinarine acts as a non-competitive inhibitor. CD and fluorescence spectroscopy results indicated towards an adequate protein conformation from pH 3.5 to 8.5. The quenching constant (Ksv) and free energy (ΔG) of LdPP2C was found to be 11.1 ± 0.2 mM-1 and 2.0 ± 1.1 kcal mol-1 in presence of acrylamide and urea respectively. The protein was found to elicit the innate immune functions through upregulation of pro-inflammatory cytokines (TNF-α and IL-6) as well as nitric oxide generation. Simultaneously, these cytokines were found to be fairly higher in protein treated cells as compared to untreated cells at transcript level too. These observations advocate that LdPP2C generates a pro-inflammatory environment in macrophages and hence plays important role in immunomodulation. Computational modelling showed similar three-dimensional structure and metal binding sites present in other member of PP2C subfamily, while docking studies revealed its interaction with substrate as well as its specific inhibitor. Our study has provided first time reports on enzyme kinetics, structural features and immune response inside the host macrophage of metal-dependent protein phosphatases from a trypanosomatid parasite.
Collapse
Affiliation(s)
- Pranay Jakkula
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad, 500046, India
| | - Rahila Qureshi
- Department of Genetics, Osmania University, Hyderabad, 500007, India
| | - Atif Iqbal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad, 500046, India
| | - S R Sagurthi
- Department of Genetics, Osmania University, Hyderabad, 500007, India
| | - Insaf A Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad, 500046, India.
| |
Collapse
|
21
|
Bandaru S, Tarigopula P, Akka J, Marri VK, Kattamuri RK, Nayarisseri A, Mangalarapu M, Vinukonda S, Mundluru HP, Sagurthi SR. Association of Beta 2 adrenergic receptor (Thr164Ile) polymorphism with Salbutamol refractoriness in severe asthmatics from Indian population. Gene 2016; 592:15-22. [PMID: 27450915 DOI: 10.1016/j.gene.2016.07.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Thr164Ile polymorphism in the ADRB2 gene encoding β2 adrenergic receptor (β2AR) has its functional consequence in declining ligand-receptor interactions and depressed coupling of β2AR to adenylcyclase. In the present study, we sought to evaluate the possible association of Thr164Ile polymorphism with asthma susceptibility, pharmacogenetic response to Salbutamol and varying degrees of severity. METHODS Three hundred and ninety eight clinically diagnosed patients and four hundred and fifty six healthy controls were enrolled in the study. Patients were classified into severity classes according to the Global Initiative for Asthma (GINA) guidelines. To assess bronchodilator response, spirometry was performed before and 15min after Salbutamol (200μg) delivery. Responders to Salbutamol were categorized if percentage reversibility was greater than or equal to 12% in them, while those showing reversibility <12% were classified as non-responders. Further, responding phenotypes were stratified into severity groups. Genotyping was carried out by ARMS-PCR technique. Statistical methods were applied to test the significance of the results. RESULTS In the present study, polymorphism was not associated with disease susceptibility however; there was significant association with non-responding asthmatics. In case of severity subsets, the polymorphism was not associated with milder subtypes; although, notable association was observed with moderate and severe asthma subtypes. In addition, the polymorphism was significantly associated with non-responding patients with severe asthma. CONCLUSIONS In south Indian population, the ADRB2 Thr164Ile polymorphism may not form susceptible variant to develop asthma, however, it can form a predictive maker for bronchodilator (Salbutamol) response in severe asthmatics.
Collapse
Affiliation(s)
- Srinivas Bandaru
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad 500 016, India; National Institute of Pharmaceutical Education and Research, Hyderabad 500 037, India
| | - Pramod Tarigopula
- Government General and Chest Hospital, Gandhi Medical College and Osmania Medical College, Hyderabad 500 038, India
| | - Jyothy Akka
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad 500 016, India
| | - Vijaya Kumar Marri
- Government General and Chest Hospital, Gandhi Medical College and Osmania Medical College, Hyderabad 500 038, India
| | - Ramesh Kumar Kattamuri
- Government General and Chest Hospital, Gandhi Medical College and Osmania Medical College, Hyderabad 500 038, India
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore 452 010, India
| | - Madhavi Mangalarapu
- Department of Genetics & Biotechnology, Osmania University, Hyderabad 500 007, India
| | - Swetha Vinukonda
- Department of Genetics & Biotechnology, Osmania University, Hyderabad 500 007, India
| | - Hema Prasad Mundluru
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad 500 016, India
| | - Someswar Rao Sagurthi
- Department of Genetics & Biotechnology, Osmania University, Hyderabad 500 007, India.
| |
Collapse
|
22
|
Devi Alaparthi M, Gopinath G, Bandaru S, Sankeshi V, Mangalarapu M, Sudha Nagamalla S, Sudhakar K, Roja Rani A, Rao Sagurthi S. Virtual screening of RAGE inhibitors using molecular docking. Bioinformation 2016; 12:124-130. [PMID: 28149046 PMCID: PMC5267955 DOI: 10.6026/97320630012124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 01/29/2016] [Revised: 04/08/2016] [Accepted: 04/09/2016] [Indexed: 11/23/2022] Open
Abstract
Advanced Glycation End products (AGEs) interaction with Receptor for AGEs (RAGE) activates downstream signaling and evokes
inflammatory responses in vascular cells. Therefore, it is of interest to design a novel series of molecules with a library of 352
compounds based on natural Isoflavone and Argpyrimidine moities. The compounds screened against the optimized structure of
RAGE (PDB code: 3CJJ) using MolDock aided with molecular docking algorithm. This exercise identified compound number 62
with appreciable ADME properties having no toxicity and pharmacophore features. Therefore, compound 62 identified as a RAGE
inhibitor is proposed for further validation in the context of Diabetic Retinopathy (DR) and vascular complications.
Collapse
Affiliation(s)
- Malini Devi Alaparthi
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Gudipudi Gopinath
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Srinivas Bandaru
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Venu Sankeshi
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Madhavi Mangalarapu
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | | | - Kota Sudhakar
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Anupalli Roja Rani
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar Rao Sagurthi
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, India
| |
Collapse
|
23
|
Bangera M, Panigrahi R, Sagurthi SR, Savithri HS, Murthy MRN. Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance. J Struct Biol 2015; 189:238-50. [PMID: 25600413 DOI: 10.1016/j.jsb.2015.01.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 11/29/2022]
Abstract
In many organisms "Universal Stress Proteins" (USPs) are induced in response to a variety of environmental stresses. Here we report the structures of two USPs, YnaF and YdaA from Salmonella typhimurium determined at 1.8Å and 2.4Å resolutions, respectively. YnaF consists of a single USP domain and forms a tetrameric organization stabilized by interactions mediated through chloride ions. YdaA is a larger protein consisting of two tandem USP domains. Two protomers of YdaA associate to form a structure similar to the YnaF tetramer. YdaA showed ATPase activity and an ATP binding motif G-2X-G-9X-G(S/T/N) was found in its C-terminal domain. The residues corresponding to this motif were not conserved in YnaF although YnaF could bind ATP. However, unlike YdaA, YnaF did not hydrolyse ATP in vitro. Disruption of interactions mediated through chloride ions by selected mutations converted YnaF into an ATPase. Residues that might be important for ATP hydrolysis could be identified by comparing the active sites of native and mutant structures. Only the C-terminal domain of YdaA appears to be involved in ATP hydrolysis. The structurally similar N-terminal domain was found to bind a zinc ion near the segment equivalent to the phosphate binding loop of the C-terminal domain. Mass spectrometric analysis showed that YdaA might bind a ligand of approximate molecular weight 800daltons. Structural comparisons suggest that the ligand, probably related to an intermediate in lipid A biosynthesis, might bind at a site close to the zinc ion. Therefore, the N-terminal domain of YdaA binds zinc and might play a role in lipid metabolism. Thus, USPs appear to perform several distinct functions such as ATP hydrolysis, altering membrane properties and chloride sensing.
Collapse
Affiliation(s)
- M Bangera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - R Panigrahi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - S R Sagurthi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - H S Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - M R N Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
24
|
Gowda G, Sagurthi SR, Savithri HS, Murthy MRN. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the mannose 6-phosphate isomerase from Salmonella typhimurium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:81-4. [PMID: 18259054 DOI: 10.1107/s1744309107067930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 12/20/2007] [Indexed: 11/10/2022]
Abstract
Mannose 6-phosphate isomerase (MPI; EC 5.3.1.8) catalyzes the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). In the eukaryotes and prokaryotes investigated to date, the enzyme has been reported to play a crucial role in D-mannose metabolism and supply of the activated mannose donor guanosine diphosphate D-mannose (GDP-D-mannose). In the present study, MPI was cloned from Salmonella typhimurium, overexpressed in Escherichia coli and purified using Ni-NTA affinity column chromatography. Purified MPI crystallized in space group P2(1)2(1)2(1), with unit-cell parameters a = 36.03, b = 92.2, c = 111.01 A. A data set extending to 1.66 A resolution was collected with 98.8% completeness using an image-plate detector system mounted on a rotating-anode X-ray generator. The asymmetric unit of the crystal cell was compatible with the presence of a monomer of MPI. A preliminary structure solution of the enzyme has been obtained by molecular replacement using Candida albicans MPI as the phasing model and the program Phaser. Further refinement and model building are in progress.
Collapse
Affiliation(s)
- Giri Gowda
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | | | | |
Collapse
|
25
|
Sagurthi SR, Panigrahi RR, Gowda G, Savithri HS, Murthy MRN. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of universal stress protein F (YnaF) from Salmonella typhimurium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:957-60. [PMID: 18007050 DOI: 10.1107/s1744309107048610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 10/03/2007] [Indexed: 11/10/2022]
Abstract
The universal stress protein UspF (YnaF) is a small cytoplasmic bacterial protein. The expression of stress proteins is enhanced when cells are exposed to heat shock, nutrition starvation and certain other stress-inducing agents. YnaF promotes cell survival during prolonged exposure to stress and may activate a general mechanism for stress endurance. This manuscript reports preliminary crystallographic studies on YnaF from Salmonella typhimurium. The gene coding for YnaF was cloned and overexpressed and the protein was purified by Ni-NTA affinity chromatography. Purified YnaF was crystallized using vapour-diffusion and microbatch methods. The crystals belong to space group P2(1), with unit-cell parameters a = 37.51, b = 77.18, c = 56.34 A, beta = 101.8 degrees . A data set was collected to 2.5 A resolution with 94.6% completeness using an image-plate detector system mounted on a rotating-anode X-ray generator. Attempts to determine the structure are in progress.
Collapse
|