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Negahdari B, Sarkoohi P, Ghasemi Nezhad F, Shahbazi B, Ahmadi K. Design of multi-epitope vaccine candidate based on OmpA, CarO and ZnuD proteins against multi-drug resistant Acinetobacter baumannii. Heliyon 2024; 10:e34690. [PMID: 39149030 PMCID: PMC11324976 DOI: 10.1016/j.heliyon.2024.e34690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
Acinetobacter baumannii has been identified as a major cause of nosocomial infections. Acinetobacter infections are often difficult to treat with multidrug resistant phenotypes. One of the most effective ways to combat infectious diseases is through vaccination. In this study, an attempt was made to select the most protective and potent immunostimulatory epitopes based on the epitope-rich domains of the ZnuD, OmpA and CarO proteins of Acinetobacter baumannii to design a vaccine that can protect against this infection. After predicting the epitope of B- and T-cells, seven antigenic regions of three proteins CarO, ZnuD and OmpA, were selected. These regions were bound by a GGGS linker. The binding affinity and molecular interactions of the vaccine with the immune receptors TLR2 and TLR4 were studied using molecular docking analysis. This vaccine design was subjected to in silico immune simulations using C-ImmSim. The designed vaccine was highly antigenic, non-allergenic and stable. TLR2 and TLR4 were selected to analyze the ability of the modeled chimeric protein to interact with immune system receptors. The results showed strong interaction between the designed protein vaccine with TLR2 (-18.8 kcal mol-1) and TLR4 (-15.1 kcal mol-1). To verify the stability of the interactions and the structure of the designed protein, molecular dynamics (MD) simulations were performed for 200 ns. Various analyses using MD showed that the protein structure is stable alone and in interaction with TLR2 and TLR4. The ability of the vaccine candidate protein to stimulate the immune system to produce the necessary cytokines and antibodies against Acinetobacter baumannii was also demonstrated by the ability of the protein designed using the C-ImmSim web server to induce an immune response. Therefore, the designed protein vaccine may be a suitable candidate for in vivo as well as in vitro studies against Acinetobacter baumannii infections.
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Affiliation(s)
- Batul Negahdari
- Student Research Committee, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Parisa Sarkoohi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Forozan Ghasemi Nezhad
- Student Research Committee, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Bojja KS, Kumar A, Palanimuthu D, Holla H, Gawli K. Inhibition and kinetic studies of phytochemical constituents of Goniothalamus wynaadensis and their isoxazoline derivatives on α-glucosidase. Nat Prod Res 2024:1-11. [PMID: 38759219 DOI: 10.1080/14786419.2024.2352140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/01/2024] [Indexed: 05/19/2024]
Abstract
α-Glucosidase, an enzyme involved in post-prandial hyperglycaemia, was used as a target to study the effect of compound(s) isolated from Goniothalamus wynaadensis and its isoxazoline derivatives. Among thirteen compounds screened, compounds 1, 3a and 3j exhibited significant inhibition with IC50 values of 63.42, 61.36 and 58.89 µg/mL, respectively, outperforming acarbose (71.72 µg/mL). Kinetic studies revealed competitive binding for compound 1 and uncompetitive/non-competitive binding for 3a and 3j. Fluorescence quenching showed a linear relationship between I0/I at different inhibitor concentrations. The binding sites in α-glucosidase were ≤ 1. The binding constants 3a (0.7307) > 3j (0.6563) > 1 (0.5415) displayed strong interactions. Docking study revealed binding affinities; 3j (-8.9) > 3a (-7.7) > 1 (-7), and acarbose, 1, 3a and 3j had ARG-312, PHE-157 interactions in common to α-glucosidase. The toxicity profile showed compounds fell in classes IV and V. Overall, the results indicate that compounds 1, 3a and 3j are effective against α-glucosidase.
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Affiliation(s)
- Kavya Sritha Bojja
- Department of Life Science, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Akash Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, Karnataka, India
| | | | - Harish Holla
- Department of Chemistry, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Kavishankar Gawli
- Department of Life Science, Central University of Karnataka, Kalaburagi, Karnataka, India
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3
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Abdullahi AD, Unban K, Saenjum C, Kodchasee P, Kangwan N, Thananchai H, Shetty K, Khanongnuch C. Antibacterial activities of Miang extracts against selected pathogens and the potential of the tannin-free extracts in the growth inhibition of Streptococcus mutans. PLoS One 2024; 19:e0302717. [PMID: 38718045 PMCID: PMC11078415 DOI: 10.1371/journal.pone.0302717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Bacterial pathogens have remained a major public health concern for several decades. This study investigated the antibacterial activities of Miang extracts (at non-neutral and neutral pH) against Bacillus cereus TISTR 747, Escherichia coli ATCC 22595, Salmonella enterica serovar Typhimurium TISTR 292 and Streptococcus mutans DMST 18777. The potential of Polyvinylpolypyrrolidone (PVPP)-precipitated tannin-free Miang extracts in growth-inhibition of the cariogenic Streptococcus mutans DMST 18777 and its biofilms was also evaluated. The tannin-rich fermented extracts had the best bacterial growth inhibition against S. mutans DMST 18777 with an MIC of 0.29 and 0.72 mg/mL for nonfilamentous fungi (NFP) Miang and filamentous-fungi-processed (FFP) Miang respectively. This observed anti-streptococcal activity still remained after PVPP-mediated precipitation of bioactive tannins especially, in NFP and FFP Miang. Characterization of the PVPP-treated extracts using High performance liquid chromatography quadrupole-time of flight-mass spectrometry (HPLC-QToF-MS) analysis, also offered an insight into probable compound classes responsible for the activities. In addition, Crystal violet-staining also showed better IC50 values for NFP Miang (4.30 ± 0.66 mg/mL) and FFP Miang (12.73 ± 0.11 mg/mL) against S. mutans DMST 18777 biofilms in vitro. Homology modeling and molecular docking analysis using HPLC-MS identified ligands in tannin-free Miang supernatants, was performed against modelled S. mutans DMST 18777 sortase A enzyme. The in silico analysis suggested that the inhibition by NFP and FFP Miang might be attributed to the presence of ellagic acid, flavonoid aglycones, and glycosides. Thus, these Miang extracts could be optimized and explored as natural active pharmaceutical ingredients (NAPIs) for applications in oral hygienic products.
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Affiliation(s)
- Aliyu Dantani Abdullahi
- Interdisciplinary Program in Biotechnology, The Graduate School, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Kridsada Unban
- Faculty of Agro-Industry, Division of Food Science and Technology, School of Agro-Industry, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Chalermpong Saenjum
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Pratthana Kodchasee
- Research Center for Multidisciplinary Approaches to Miang, Multidisciplinary Research Institute (MDRI), Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Napapan Kangwan
- Division of Physiology, School of Medical Sciences, University of Phayao, Phayao, Thailand
| | - Hathairat Thananchai
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Kalidas Shetty
- Faculty of Agriculture, Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Chartchai Khanongnuch
- Research Center for Multidisciplinary Approaches to Miang, Multidisciplinary Research Institute (MDRI), Chiang Mai University, Muang, Chiang Mai, Thailand
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
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Mahapatra K. Unveiling the structure and interactions of SOG1, a NAC domain transcription factor: An in-silico perspective. J Genet Eng Biotechnol 2024; 22:100333. [PMID: 38494249 PMCID: PMC10980851 DOI: 10.1016/j.jgeb.2023.100333] [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: 03/19/2024]
Abstract
SOG1 is a crucial plant-specific NAC domain family transcription factor and functions as the central regulator of DNA damage response, acting downstream of ATM and ATR kinases. In this study, various in-silico approaches have been employed for the characterization of SOG1 transcription factor in a comparative manner with its orthologues from various plant species. Amino acid sequences of more than a hundred SOG1 or SOG1-like proteins were retrieved and their relationship was determined through phylogenetic and motif analyses. Various physiochemical properties and secondary structural components of SOG1 orthologues were determined in selective plant species including Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, and Physcomitrella patens. Furthermore, fold recognition or threading and homology-based three-dimensional models of SOG1 were constructed followed by subsequent evaluation of quality and accuracy of the generated protein models. Finally, extensive DNA-Protein and Protein-Protein interaction studies were performed using the HADDOCK server to give an insight into the mechanism of how SOG1 binds with the promoter region of its target genes or interacts with other proteins to regulate the DNA damage responses in plants. Our docking analysis data have shown the molecular mechanism of SOG1's binding with 5'-CTT(N)7AAG-3' and 5'-(N)4GTCAA(N)4-3' consensus sequences present in the promoter region of its target genes. Moreover, SOG1 physically interacts and forms a thermodynamically stable complex with NAC103 and BRCA1 proteins, which possibly serve as coactivators or mediators in the transcription regulatory network of SOG1. Overall, our in-silico study will provide meaningful information regarding the structural and functional characterization of the SOG1 transcription factor.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan - 713 104, West Bengal, India.
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Bajia D, Derwich K. An In Silico Study Investigating Camptothecin-Analog Interaction with Human Protein Tyrosine Phosphatase, SHP2 (PTPN11). Pharmaceuticals (Basel) 2023; 16:926. [PMID: 37513838 PMCID: PMC10386118 DOI: 10.3390/ph16070926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The human PTPN11 gene encodes for the src tyrosine phosphatase protein (SHP2) is now gaining much attention in many disorders, particularly its oncogenic involvement in many types of cancer. Efforts in developing molecules targeting SHP2 with high efficacy are the future of drug discovery and chemotherapy. However, the interaction of a new camptothecin analog with the catalytic domain of SHP2 protein remains unknown. Therefore, this study aims to provide in silico rationale for the recognition and binding of FL118 and irinotecan with the catalytic domain of human protein tyrosine phosphatase-SHP2 (PTPc-SH2-SHP2, chain A). The docking interaction of the human SHP2 protein's catalytic domain as well as Y279C and R465G mutants with FL118 and irinotecan ligands were calculated and analyzed using the Autodock 4.2 programme, setting the docking grid to target the protein's active site. The camptothecin analog FL118 had the best lowest negative affinity energies with PTPc-SHP2 wildtype and SHP2-Y279C mutant model (-7.54 Kcal/mol and -6.94 Kcal/mol, respectively). Moreover, the protein-ligand complexes revealed several hydrogen bond interactions reflecting the degree of stability that each structure possesses, with the FL118-SHP2-wildtype forming the most stable complex among the structures. In addition, the FL118-SHP2 wildtype complex was validated for RMSD, RMSF, hydrogen bonds, and salt bridges. This revealed that the complex generated became stable over time. This in silico rationale identifies the novel FL118 camptothecin analog as a potent selective inhibitor of PTPc-SH2 domain of SHP2 protein, paving way for further in vitro investigations into the interactions and binding activity of analogs with SHP2 for potential therapeutic applications in PTPN11-associated disorders.
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Affiliation(s)
- Donald Bajia
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, Ul. Fredry 10, 61701 Poznan, Poland
| | - Katarzyna Derwich
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, Ul. Fredry 10, 61701 Poznan, Poland
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6
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Molecular Design and In-Silico Analysis of Trisubstituted Benzimidazole Derivatives as Ftsz Inhibitor. J CHEM-NY 2023. [DOI: 10.1155/2023/9307613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Tuberculosis (TB) is the fastest spreading infectious disease and one of the top ten diseases that kill millions of people annually. The rapid spread of a multidrug-resistant strain of Mycobacterium tuberculosis leads to multidrug-resistance tuberculosis (MDR-TB), which is very difficult to treat. Filament temperature-sensitive protein ring-Z (Ftsz) protein could be the best target to inhibit bacterial cytokinesis. This research is conducted to predict the antitubercular activity of trisubstituted benzimidazole derivatives targeting FtsZ protein by an in-silico approach (molecular docking, pharmacokinetic parameter, drug likeliness, toxicity prediction, and biological activity prediction). Amine and aldehyde substitutions are used as primary scaffolds to design 20 trisubstituted benzimidazole derivatives for molecular docking. AutoDock vina v.1.2.0 software was used to predict the binding interaction between ligand and receptor (FtsZ, PDB ID : 1RQ7). The drug-likeliness properties and toxicity of ligands were predicted from SwissADMET and ToxiM web servers, respectively. Compound A15 (2,3,5,6-tetrafluoro-N1-{6-fluoro-5-[4-(1H-imidazole-1-yl) phenoxy]-1H-1,3-benzodiazol-2-yl} benzene-1,4-diamine) showed the best binding energy (ΔG = −10.2 kcal/mol/) along with four hydrogen bond interactions (GLY107, PHE180, ASP 184). Similarly, compounds A19 and A20 have the best binding score of −9.8 kcal/mol, with excellent pharmacokinetic parameters. It is found that the binding energy of all ligands (ΔG = −8.0 to −10.2 kcal/mol) is better than the reference compound Moxifloxacin (ΔG = −7.7 kcal/mol). None of the ligands violate Lipinski’s rule, but all ligands’ toxicity is slightly high (>0.8 score). It is reported that the amine-substituted benzimidazole derivatives have better binding energy than the aldehyde substitution. Therefore, it is concluded that compounds A19 and A20 can be the best candidate as Ftsz protein inhibitors but an in-vitro animal study and toxicity study are necessary to validate these data.
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7
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In silico protein engineering shows that novel mutations affecting NAD + binding sites may improve phosphite dehydrogenase stability and activity. Sci Rep 2023; 13:1878. [PMID: 36725973 PMCID: PMC9892502 DOI: 10.1038/s41598-023-28246-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Pseudomonas stutzeri phosphite dehydrogenase (PTDH) catalyzes the oxidation of phosphite to phosphate in the presence of NAD, resulting in the formation of NADH. The regeneration of NADH by PTDH is greater than any other enzyme due to the substantial change in the free energy of reaction (G°' = - 63.3 kJ/mol). Presently, improving the stability of PTDH is for a great importance to ensure an economically viable reaction process to produce phosphite as a byproduct for agronomic applications. The binding site of NAD+ with PTDH includes thirty-four residues; eight of which have been previously mutated and characterized for their roles in catalysis. In the present study, the unexplored twenty-six key residues involved in the binding of NAD+ were subjected to in silico mutagenesis based on the physicochemical properties of the amino acids. The effects of these mutations on the structure, stability, activity, and interaction of PTDH with NAD+ were investigated using molecular docking, molecular dynamics simulations, free energy calculations, and secondary structure analysis. We identified seven novel mutations, A155I, G157I, L217I, P235A, V262I, I293A, and I293L, that reduce the compactness of the protein while improving PTDH stability and binding to NAD+.
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Chowdhury AT, Hasan MN, Bhuiyan FH, Islam MQ, Nayon MRW, Rahaman MM, Hoque H, Jewel NA, Ashrafuzzaman M, Prodhan SH. Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions. PLoS One 2023; 18:e0273592. [PMID: 37163561 PMCID: PMC10171694 DOI: 10.1371/journal.pone.0273592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/27/2023] [Indexed: 05/12/2023] Open
Abstract
Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)-cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.
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Affiliation(s)
- Aniqua Tasnim Chowdhury
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Fahmid H Bhuiyan
- Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Md Qamrul Islam
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Rakib Wazed Nayon
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Mashiur Rahaman
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Ashrafuzzaman
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Shamsul H Prodhan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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Oselusi S, Fadaka AO, Wyckoff GJ, Egieyeh SA. Computational Target-Based Screening of Anti-MRSA Natural Products Reveals Potential Multitarget Mechanisms of Action through Peptidoglycan Synthesis Proteins. ACS OMEGA 2022; 7:37896-37906. [PMID: 36312373 PMCID: PMC9609086 DOI: 10.1021/acsomega.2c05061] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/06/2022] [Indexed: 05/22/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of bacterial infections in both healthcare and community settings. MRSA can acquire resistance to any current antibiotic, which has major implications for its current and future treatment options. As such, it is globally a major focus for infection control efforts. The mechanical rigidity provided by peptidoglycans in the bacteria cell walls makes it a promising target for broad-spectrum antibacterial drug discovery. The development of drugs that can target different stages of the synthesis of peptidoglycan in MRSA may compromise the integrity of its cell wall and consequently result in the rapid decline of diseases associated with this drug-resistant bacteria. The present study is aimed at screening natural products with known in vitro activities against MRSA to identify their potential to inhibit the proteins involved in the biosynthesis of the peptidoglycan cell wall. A total of 262 compounds were obtained when a literature survey was conducted on anti-MRSA natural products (AMNPs). Virtual screening of the AMNPs was performed against various proteins (targets) that are involved in the biosynthesis of the peptidoglycan (PPC) cell wall using Schrödinger software (release 2020-3) to determine their binding affinities. Nine AMNPs were identified as potential multitarget inhibitors against peptidoglycan biosynthesis proteins. Among these compounds, DB211 showed the strongest binding affinity and interactions with six protein targets, representing three stages of peptidoglycan biosynthesis, and thus was selected as the most promising compound. The MD simulation results for DB211 and its proteins indicated that the protein-ligand complexes were relatively stable over the simulation period of 100 ns. In conclusion, DB211 showed the potential to inhibit six proteins involved in the biosynthesis of the peptidoglycan cell wall in MRSA, thus reducing the chance of MRSA developing resistance to this compound. Therefore, DB211 provided a starting point for the design of new compounds that can inhibit multiple targets in the biosynthesis of the peptidoglycan layer in MRSA.
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Affiliation(s)
- Samson
Olaitan Oselusi
- University
of the Western Cape, School of Pharmacy,
Faculty of Natural Sciences, Robert Sobukwe Road, Bellville, Cape Town, Western Cape ZA 7535, South Africa
| | - Adewale Oluwaseun Fadaka
- University
of the Western Cape, Science and Innovation/Mintek
Nanotechnology Innovation Centre, Department of Biotechnology, Faculty
of Natural Sciences, Robert
Sobukwe Road, Bellville, Cape Town, Western Cape ZA 7535, South Africa
| | - Gerald J. Wyckoff
- University
of Missouri Kansas City, School of Pharmacy,
Division of Pharmacology and Pharmaceutical Sciences, 5000 Holmes Street, Kansas
City, Missouri 64110-2446, United States
| | - Samuel Ayodele Egieyeh
- University
of the Western Cape, School of Pharmacy,
Faculty of Natural Sciences, Robert Sobukwe Road, Bellville, Cape Town, Western Cape ZA 7535, South Africa
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10
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Nordquist EB, Clerico EM, Chen J, Gierasch LM. Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future. J Phys Chem B 2022; 126:6780-6791. [PMID: 36040440 PMCID: PMC10309085 DOI: 10.1021/acs.jpcb.2c03806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70-client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of "selective promiscuity" in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Eugenia M. Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Lila M. Gierasch
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
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11
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Ricatti J, Acquasaliente L, Ribaudo G, De Filippis V, Bellini M, Llovera RE, Barollo S, Pezzani R, Zagotto G, Persaud KC, Mucignat-Caretta C. Effects of point mutations in the binding pocket of the mouse major urinary protein MUP20 on ligand affinity and specificity. Sci Rep 2019; 9:300. [PMID: 30670733 PMCID: PMC6342991 DOI: 10.1038/s41598-018-36391-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/15/2018] [Indexed: 12/30/2022] Open
Abstract
The mouse Major Urinary Proteins (MUPs) contain a conserved β-barrel structure with a characteristic central hydrophobic pocket that binds a variety of volatile compounds. After release of urine, these molecules are slowly emitted in the environment where they play an important role in chemical communication. MUPs are highly polymorphic and conformationally stable. They may be of interest in the construction of biosensor arrays capable of detection of a broad range of analytes. In this work, 14 critical amino acids in the binding pocket involved in ligand interactions were identified in MUP20 using in silico techniques and 7 MUP20 mutants were synthesised and characterised to produce a set of proteins with diverse ligand binding profiles to structurally different ligands. A single amino acid substitution in the binding pocket can dramatically change the MUPs binding affinity and ligand specificity. These results have great potential for the design of new biosensor and gas-sensor recognition elements.
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Affiliation(s)
- Jimena Ricatti
- Department of Molecular Medicine, University of Padua, Padua, Italy.,Cell Biology and Neuroscience Institute, University of Buenos Aires-National Scientific and Technical Council (UBA-CONICET), Buenos Aires, Argentina
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Marino Bellini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Ramiro Esteban Llovera
- Multidisciplinary Institute of Cell Biology, National Scientific and Technical Council (CONICET) and Department of Science and Technology, National University of Quilmes, Buenos Aires, Argentina
| | - Susi Barollo
- Department of Medicine, University of Padua, Padua, Italy
| | | | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Krishna C Persaud
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, UK
| | - Carla Mucignat-Caretta
- Department of Molecular Medicine, University of Padua, Padua, Italy. .,National Institute of Biostructures and Biosystems, Rome, Italy.
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12
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Ahmad S, Raza S, Abro A, Liedl KR, Azam SS. Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme. J Biomol Struct Dyn 2018; 37:1326-1345. [DOI: 10.1080/07391102.2018.1459318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Asma Abro
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Faculty of Life Sciences and Informatics, Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Klaus R. Liedl
- Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
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13
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Saxena S, Abdullah M, Sriram D, Guruprasad L. Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:3184-3198. [PMID: 28948866 DOI: 10.1080/07391102.2017.1384398] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.
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Affiliation(s)
- Shalini Saxena
- a School of Chemistry , University of Hyderabad , Hyderabad 500046 , India
| | - Maaged Abdullah
- a School of Chemistry , University of Hyderabad , Hyderabad 500046 , India
| | - Dharmarajan Sriram
- b Computer Aided Drug Design Laboratory, Department of Pharmacy , Birla Institute of Technology & Science-Pilani, Hyderabad Campus , Hyderabad 500078 , India
| | - Lalitha Guruprasad
- a School of Chemistry , University of Hyderabad , Hyderabad 500046 , India
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14
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Sang P, Hu W, Ye YJ, Li LH, Zhang C, Xie YH, Meng ZH. In silico screening, molecular docking, and molecular dynamics studies of SNP-derived human P5CR mutants. J Biomol Struct Dyn 2017; 35:2441-2453. [PMID: 27677826 DOI: 10.1080/07391102.2016.1222967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/07/2016] [Indexed: 01/13/2023]
Abstract
Pyrroline-5-carboxylate reductase (P5CR) encoded by PYCR1 gene is a housekeeping enzyme that catalyzes the reduction of P5C to proline using NAD(P)H as the cofactor. In this study, we used in silico approaches to examine the role of nonsynonymous single-nucleotide polymorphisms in the PYCR1 gene and their putative functions in the pathogenesis of Cutis Laxa. Among the 348 identified SNPs, 15 were predicted to be potentially damaging by both SIFT and PolyPhen tools; of them two SNP-derived mutations, R119G and G206W, have been previously reported to correlate with Cutis Laxa. These two mutations were therefore selected to be mapped to the wild-type (WT) P5CR structure for further structural and functional analyses. The results of comparative computational analyses using I-Mutant and Autodock reveal reductions in both stability and cofactor binding affinity of these two mutants. Comparative molecular dynamics (MD) simulations were performed to evaluate the changes in dynamic properties of P5CR upon mutations. The results reveal that the two mutations enhance the rigidity of P5CR structure, especially that of cofactor binding site, which could result in decreased kinetics of cofactor entrance and egress. Comparison between the structural properties of the WT and mutants during MD simulations shows that the enhanced rigidity of mutants results most likely from the increased number of inter-atomic interactions and the decreased number of dynamic hydrogen bonds. Our study provides novel insight into the deleterious effects of the R119G and G206W mutations on P5CR, and sheds light on the mechanisms by which these mutations mediate Cutis Laxa.
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Affiliation(s)
- Peng Sang
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Wei Hu
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Yu-Jia Ye
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Lin-Hua Li
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Chao Zhang
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Yue-Hui Xie
- b Department of Computer Science, The Faculty of Basic Medicine , Kunming Medical University , Kunming , P.R China
| | - Zhao-Hui Meng
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
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15
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Pharmacoinformatics study of Piperolactam A from Piper betle root as new lead for non steroidal anti fertility drug development. Comput Biol Chem 2017; 67:213-224. [DOI: 10.1016/j.compbiolchem.2017.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 06/19/2016] [Accepted: 01/09/2017] [Indexed: 11/22/2022]
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16
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Synthesis, Bioevaluation and Molecular Dynamic Simulation Studies of Dexibuprofen-Antioxidant Mutual Prodrugs. Int J Mol Sci 2016; 17:ijms17122151. [PMID: 28009827 PMCID: PMC5187951 DOI: 10.3390/ijms17122151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/14/2016] [Accepted: 12/14/2016] [Indexed: 02/02/2023] Open
Abstract
Dexibuprofen–antioxidant conjugates were synthesized with the aim to reduce its gastrointestinal effects. The esters analogs of dexibuprofen 5a–c were obtained by reacting its –COOH group with chloroacetyl derivatives 3a–c. The in vitro hydrolysis data confirmed that synthesized prodrugs 5a–c were stable in stomach while undergo significant hydrolysis in 80% human plasma and thus release free dexibuprofen. The minimum reversion was observed at pH 1.2 suggesting that prodrugs are less irritating to stomach than dexibuprofen. The anti-inflammatory activity of 5c (p < 0.001) is more significant than the parent dexibuprofen. The prodrug 5c produced maximum inhibition (42.06%) of paw-edema against egg-albumin induced inflammation in mice. Anti-pyretic effects in mice indicated that prodrugs 5a and 5b showed significant inhibition of pyrexia (p < 0.001). The analgesic activity of 5a is more pronounced compared to other synthesized prodrugs. The mean percent inhibition indicated that the prodrug 5a was more active in decreasing the number of writhes induced by acetic acid than standard dexibuprofen. The ulcerogenic activity results assured that synthesized prodrugs produce less gastrointestinal adverse effects than dexibuprofen. The ex vivo antiplatelet aggregation activity results also confirmed that synthesized prodrugs are less irritant to gastrointestinal mucosa than the parent dexibuprofen. Molecular docking analysis showed that the prodrugs 5a–c interacts with the residues present in active binding sites of target protein. The stability of drug–target complexes is verified by molecular dynamic simulation study. It exhibited that synthesized prodrugs formed stable complexes with the COX-2 protein thus support our wet lab results. It is therefore concluded that the synthesized prodrugs have promising pharmacological activities with reduced gastrointestinal adverse effects than the parent drug.
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17
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Structural exploration of PPARγ modulators through pharmacophore mapping, fragment-based design, docking, and molecular dynamics simulation analyses. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Fakhar Z, Naiker S, Alves CN, Govender T, Maguire GEM, Lameira J, Lamichhane G, Kruger HG, Honarparvar B. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis. J Biomol Struct Dyn 2016; 34:2399-417. [PMID: 26612108 DOI: 10.1080/07391102.2015.1117397] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.
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Affiliation(s)
- Zeynab Fakhar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Suhashni Naiker
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Claudio N Alves
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa.,c School of Chemistry and Physics , University of KwaZulu-Natal , 4001 Durban , South Africa
| | - Jeronimo Lameira
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Gyanu Lamichhane
- d Division of Infectious Diseases, Center for Tuberculosis Research , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Bahareh Honarparvar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
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19
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Kumar A, Randhawa V, Acharya V, Singh K, Kumar S. Amino acids flanking the central core of Cu,Zn superoxide dismutase are important in retaining enzyme activity after autoclaving. J Biomol Struct Dyn 2016; 34:475-85. [DOI: 10.1080/07391102.2015.1049551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Verma K, Ramanathan K. Investigation of Paclitaxel Resistant R306C Mutation in β-Tubulin—A Computational Approach. J Cell Biochem 2016; 116:1318-24. [PMID: 25735511 DOI: 10.1002/jcb.25087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/16/2015] [Indexed: 11/12/2022]
Abstract
Paclitaxel is the most effective chemotherapeutic agent used for the treatment of a broad spectrum of solid tumors. However, observed paclitaxel resistance in clinical trials presents one of the major obstacles for cancer chemotherapy. Most importantly, resistance due to β-tubulin mutations (R306C) has been intensely debated in recent years. Despite all efforts, mechanism of resistance is still not well understood. In this study, computational techniques were employed to uncover the effect of R306C mutation in the β-tubulin structure and its function. The tools such as I-Mutant, CUPSAT and Fold-X were employed to address the consequence of R306C mutation in the structural stability of β-tubulin. Further, molecular docking and molecular dynamics study was employed to understand the functional impact of β-tubulin mutation. Our results suggest that the R306C mutation causes a significant reduction in the binding affinity between β-tubulin and paclitaxel. Further, docked complex analysis indicates that destruction of conservative hydrogen bond maintained by the residues Arg282 and Gly360 should be responsible for the large conformation changes of the binding pocket in R306C mutant. Finally, molecular dynamics simulations study confirms the stable binding of paclitaxel with native type β-tubulin structure rather than mutant (R306C) type. We certainly believe that this study will provide useful guidance for the development of novel inhibitors that are less susceptible to drug resistance.
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Affiliation(s)
- Kanika Verma
- Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - K Ramanathan
- Industrial Biotechnology Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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Elengoe A, Naser MA, Hamdan S. Molecular dynamics simulation and docking studies on novel mutants (T11V, T12P and D364S) of the nucleotide-binding domain of human heat shock 70 kDa protein. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Sánchez-Guerrero E, Hernández-Campos ME, Correa-Basurto J, López-Sánchez P, Tolentino-López LE. Three-dimensional structure and molecular dynamics studies of prorrenin/renin receptor: description of the active site. MOLECULAR BIOSYSTEMS 2015; 11:2520-8. [PMID: 26177886 DOI: 10.1039/c5mb00342c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recent finding of a specific receptor for prorrenin/renin (PRR) has brought new insights into the physiology of the renin-angiotensin-aldosterone system. No undoubtable role has been described for this receptor so far. Its role seems to be important in chronic illnesses such as hypertension, possibly participating in the cardiovascular remodeling process, and diabetes where participation in inflammation development has been described. It is not possible, however, to explore the PRR function using classical pharmacological approaches due to the lack of specific agonists or antagonists. Two synthetic peptides have been described to accomplish these roles, but no conclusive data have been provided. There are no X-ray crystallography studies available to describe the structure and potential sites for drug development. So, the aim of this work was to model and theoretically describe the PRR. We describe and characterize the whole receptor protein, its spatial conformation and the potential interactions of PRR with the synthetic peptides available, describing the amino acid residues responsible for these interactions. This information provides the basis for directed development of drugs, seeking to agonize or antagonize PRR activity and study its function in health and ill stages.
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Affiliation(s)
- E Sánchez-Guerrero
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del IPN, Plan de San Luis y Díaz Mirón, Casco de Santo Tomás, México D.F. 11340, Mexico
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Exploring the impact of F270V mutation in the β-tubulin (Bos Taurus) structure and its function: a computational perspective. Biotechnol Lett 2015; 37:1003-11. [DOI: 10.1007/s10529-015-1765-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
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Hao W, Ji F, Wang J, Zhang Y, Wang T, Bao Y. Biochemical characterization of unusual meso-2,3-butanediol dehydrogenase from a strain of Bacillus subtilis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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