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Marimuthu SCV, Murugesan J, Babkiewicz E, Maszczyk P, Sankaranarayanan M, Thangamariappan E, Rosy JC, Ram Kumar Pandian S, Kunjiappan S, Balakrishnan V, Sundar K. Pharmacoinformatics-Based Approach for Uncovering the Quorum-Quenching Activity of Phytocompounds against the Oral Pathogen, Streptococcus mutans. Molecules 2023; 28:5514. [PMID: 37513386 PMCID: PMC10383507 DOI: 10.3390/molecules28145514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Streptococcus mutans, a gram-positive oral pathogen, is the primary causative agent of dental caries. Biofilm formation, a critical characteristic of S. mutans, is regulated by quorum sensing (QS). This study aimed to utilize pharmacoinformatics techniques to screen and identify effective phytochemicals that can target specific proteins involved in the quorum sensing pathway of S. mutans. A computational approach involving homology modeling, model validation, molecular docking, and molecular dynamics (MD) simulation was employed. The 3D structures of the quorum sensing target proteins, namely SecA, SMU1784c, OppC, YidC2, CiaR, SpaR, and LepC, were modeled using SWISS-MODEL and validated using a Ramachandran plot. Metabolites from Azadirachta indica (Neem), Morinda citrifolia (Noni), and Salvadora persica (Miswak) were docked against these proteins using AutoDockTools. MD simulations were conducted to assess stable interactions between the highest-scoring ligands and the target proteins. Additionally, the ADMET properties of the ligands were evaluated using SwissADME and pkCSM tools. The results demonstrated that campesterol, meliantrol, stigmasterol, isofucosterol, and ursolic acid exhibited the strongest binding affinity for CiaR, LepC, OppC, SpaR, and Yidc2, respectively. Furthermore, citrostadienol showed the highest binding affinity for both SMU1784c and SecA. Notably, specific amino acid residues, including ASP86, ARG182, ILE179, GLU143, ASP237, PRO101, and VAL84 from CiaR, LepC, OppC, SecA, SMU1784c, SpaR, and YidC2, respectively, exhibited significant interactions with their respective ligands. While the docking study indicated favorable binding energies, the MD simulations and ADMET studies underscored the substantial binding affinity and stability of the ligands with the target proteins. However, further in vitro studies are necessary to validate the efficacy of these top hits against S. mutans.
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Affiliation(s)
| | - Jayaprabhakaran Murugesan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil 626126, India
| | - Ewa Babkiewicz
- Department of Hydrobiology, Faculty of Biology, University of Warsaw, 02-089 Warsaw, Poland
- Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | - Piotr Maszczyk
- Department of Hydrobiology, Faculty of Biology, University of Warsaw, 02-089 Warsaw, Poland
| | - Murugesan Sankaranarayanan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani 333031, India
| | | | - Joseph Christina Rosy
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil 626126, India
| | | | - Selvaraj Kunjiappan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil 626126, India
| | - Vanavil Balakrishnan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil 626126, India
| | - Krishnan Sundar
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil 626126, India
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Roy Chowdhury D, Ghosh R, Debnath S, Bhaumik S. Potential peptidyl arginine deiminase type 4 inhibitors from Morinda citrifolia: a structure-based drug design approach. In Silico Pharmacol 2023; 11:13. [PMID: 37153695 PMCID: PMC10154455 DOI: 10.1007/s40203-023-00147-3] [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: 02/14/2023] [Accepted: 04/09/2023] [Indexed: 05/10/2023] Open
Abstract
The World Health Organization estimates that more than 23 million individuals worldwide suffer from rheumatoid arthritis (RA), a chronic systemic autoimmune disease and experts predict that the number of RA patients may double by 2030. A substantial portion of RA patients do not respond effectively to the treatment that are already available therefore there is an urgent need of innovative new drugs. Over the past several years, Peptidyl Arginine Deiminase Type 4 (PAD4) receptors have become potential therapeutic targets for the treatment of RA. The main objective of the present study is to identify potential PAD4 inhibitors from edible fruits Morinda citrifolia. Structure based virtual screening (VS) of 60 compounds from M. citrifolia were performed to identify PAD4 inhibitors. The virtual screening of compounds resulted ten hits having XP-Glide score greater than the co-ligand (XPGS: - 8.341 kcal/mol). Three hits NF_15, NF_34, and NF_35 exhibited admirable MM-GBSA dG binding energy - 52.577, - 46.777, and - 60.711 kcal/mol, respectively. These three compounds were chosen for 100 ns molecular dynamics (MD) simulations in order to evaluate the stability and interactions. The protein-ligand complex with the highest level of stability was revealed to be NF_35. Therefore, M. citrifolia fruits may be beneficial in the treatment and prevention of rheumatoid arthritis since it contains potential hits. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00147-3.
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Affiliation(s)
| | - Rajat Ghosh
- Department of Pharmacy, Tripura University, Suryamani Nagar, Agartala, Tripura 799022 India
| | - Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidyalaya, Udaipur, 799114 India
| | - Samhita Bhaumik
- Department of Chemistry, Womens College, Agartala, Tripura 799001 India
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Ahamad S, Hema K, Gupta D. Identification of Novel Tau-Tubulin Kinase 2 Inhibitors Using Computational Approaches. ACS OMEGA 2023; 8:13026-13037. [PMID: 37065061 PMCID: PMC10099139 DOI: 10.1021/acsomega.3c00225] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Tau tubulin kinase 2 (TTBK2) associated with multiple diseases is one of the kinases which phosphorylates tau and tubulin. Numerous efforts have been made to understand the role of TTBK2 in protein folding mechanisms and misfolding behavior. The misfolded protein intermediates form polymers with unwanted aggregation properties that initiate several diseases, including Alzheimer's. The availability of TTBK2 inhibitors can enhance the understanding of the molecular mechanism of action of the kinase and assist in developing novel therapeutics. In the quest for TTBK2 inhibitors, this study focuses on screening two chemical libraries (ChEMBL and ZINC-FDA). The molecular docking, RO5/absorption, distribution, metabolism, and excretion/toxicity, density functional theory, molecular dynamics (MD) simulations, and molecular mechanics with generalized Born and surface area solvation techniques enabled shortlisting of the four most active compounds, namely, ChEMBL1236395, ChEMBL2104398, ChEMBL3427435, and ZINC000000509440. Moreover, 500 ns MD simulation was performed for each complex, which provided valuable insights into the structural changes in the complexes. The relative fluctuation, solvent accessible surface area, atomic gyration, compactness covariance, and free energy landscapes revealed that the compounds could stabilize the TTBK2 protein. Overall, this study would be valuable for the researchers targeting the development of novel TTBK2 inhibitors.
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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Affiliation(s)
- Sebastian L. Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Eric J.N. Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
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Debnath P, Bhaumik S, Sen D, Muttineni RK, Debnath S. Identification of SARS-CoV-2 Main Protease Inhibitors Using Structure Based Virtual Screening and Molecular Dynamics Simulation of DrugBank Database. ChemistrySelect 2021; 6:4991-5013. [PMID: 34541295 PMCID: PMC8441713 DOI: 10.1002/slct.202100854] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is highly pathogenic to humans and has created an unprecedented global health care threat. Globally, intense efforts are going on to discover a vaccine or new drug molecules to control the COVID-19. However, till today, there is no effective therapeutics or treatment available for COVID-19. In this study, we aim to find out potential small molecule inhibitors for SARS-CoV-2 main protease (Mpro) from the known DrugBank database version 5.1.8. We applied structure-based virtual screening of the database containing 11875 numbers of drug candidates to identify potential hits for SARS-CoV-2 Mpro inhibitors. Seven potential inhibitors having admirable XP glide score ranging from -15.071 to -8.704 kcal/mol and good binding affinity with the active sites amino acids of Mpro were identified. The selected hits were further analyzed with 50 ns molecular dynamics (MD) simulation to examine the stability of protein-ligand complexes. The root mean square deviation and potential energy plot indicates the stability of the complexes during the 50 ns MD simulation. The MM-GBSA analysis also showed good binding energy of the selected hits (-83.2718 to -58.6618 kcal/mol). Further analysis revealed critical hydrogen bonds and hydrophobic interactions between compounds and the target protein. The compounds bind to biologically important regions of Mpro, indicating their potential to inhibit the functionality of this component.
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Affiliation(s)
- Pradip Debnath
- Department of ChemistryMaharaja Bir Bikram CollegeAgartalaTripura799004India
| | - Samhita Bhaumik
- Department of ChemistryWomen's CollegeAgartalaTripura799001India
| | - Debanjan Sen
- BCDA College of Pharmacy & TechnologyJessore Road South, HridaypurKolkataWest Bengal700127India
| | | | - Sudhan Debnath
- Department of ChemistryMaharaja Bir Bikram CollegeAgartalaTripura799004India
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Panwar U, Singh SK. Identification of Novel Pancreatic Lipase Inhibitors Using In Silico Studies. Endocr Metab Immune Disord Drug Targets 2020; 19:449-457. [PMID: 30484411 DOI: 10.2174/1871530319666181128100903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 05/26/2018] [Accepted: 06/27/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Obesity is well known multifactorial disorder towards the public health concern in front of the world. Increasing rates of obesity are characterized by liver diseases, chronic diseases, diabetes mellitus, hypertension and stroke, improper function of the heart, reproductive and gastrointestinal diseases, and gallstones. An essential enzyme pancreatic lipase recognized for the digestion and absorption of lipids can be a promising drug target towards the future development of antiobesity therapeutics in the cure of obesity disorders. OBJECTIVE The purpose of present study is to identify an effective potential therapeutic agent for the inhibition of pancreatic lipase. METHODS A trio of in-silico procedure of HTVS, SP and XP in Glide module, Schrodinger with default parameters, was applied on Specs databases to identify the best potential compound based on receptor grid. Finally, based on binding interaction, docking score and glide energy, selected compounds were taken forward to the platform of IFD, ADME, MMGBSA, DFT, and MDS for analyzing the ligands behavior into the protein binding site. RESULTS Using in silico protocol of structure-based virtual screening on pancreatic lipase top two compounds AN-465/43369242 & AN-465/43384139 from Specs database were reported. The result suggested that both the compounds are competitive inhibitors with higher docking score and greatest binding affinity than the reported inhibitor. CONCLUSION We anticipate that results could be future therapeutic agents and may present an idea toward the experimental studies against the inhibition of pancreatic lipase.
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Affiliation(s)
- Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
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Computational characterization of deleterious SNPs in Toll-like receptor gene that potentially cause mastitis in dairy cattle. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Panwar U, Singh SK. An Overview on Zika Virus and the Importance of Computational Drug Discovery. JOURNAL OF EXPLORATORY RESEARCH IN PHARMACOLOGY 2018; 3:43-51. [DOI: 10.14218/jerp.2017.00025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Luo H, Liang DF, Bao MY, Sun R, Li YY, Li JZ, Wang X, Lu KM, Bao JK. In silico identification of potential inhibitors targeting Streptococcus mutans sortase A. Int J Oral Sci 2018; 9:53-62. [PMID: 28358034 PMCID: PMC5379162 DOI: 10.1038/ijos.2016.58] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2016] [Indexed: 02/08/2023] Open
Abstract
Dental caries is one of the most common chronic diseases and is caused by acid fermentation of bacteria adhered to the teeth. Streptococcus mutans (S. mutans) utilizes sortase A (SrtA) to anchor surface proteins to the cell wall and forms a biofilm to facilitate its adhesion to the tooth surface. Some plant natural products, especially several flavonoids, are effective inhibitors of SrtA. However, given the limited number of inhibitors and the development of drug resistance, the discovery of new inhibitors is urgent. Here, the high-throughput virtual screening approach was performed to identify new potential inhibitors of S. mutans SrtA. Two libraries were used for screening, and nine compounds that had the lowest scores were chosen for further molecular dynamics simulation, binding free energy analysis and absorption, distribution, metabolism, excretion and toxicity (ADMET) properties analysis. The results revealed that several similar compounds composed of benzofuran, thiadiazole and pyrrole, which exhibited good affinities and appropriate pharmacokinetic parameters, were potential inhibitors to impede the catalysis of SrtA. In addition, the carbonyl of these compounds can have a key role in the inhibition mechanism. These findings can provide a new strategy for microbial infection disease therapy.
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Affiliation(s)
- Hao Luo
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Dan-Feng Liang
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Min-Yue Bao
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Rong Sun
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Yuan-Yuan Li
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Jian-Zong Li
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Xin Wang
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Kai-Min Lu
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Jin-Ku Bao
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China.,State Key Laboratory of Biotherapy/Collaborative Innovation Centre for Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Suryanarayanan V, Panwar U, Chandra I, Singh SK. De Novo Design of Ligands Using Computational Methods. Methods Mol Biol 2018; 1762:71-86. [PMID: 29594768 DOI: 10.1007/978-1-4939-7756-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
De novo design technique is complementary to high-throughput virtual screening and is believed to contribute in pharmaceutical development of novel drugs with desired properties at a very low cost and time-efficient manner. In this chapter, we outline the basic de novo design concepts based on computational methods with an example.
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Affiliation(s)
- Venkatesan Suryanarayanan
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ishwar Chandra
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India.
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Panwar U, Singh SK. Structure-based virtual screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and human lens epithelium-derived growth factor (LEDGF/p75). J Biomol Struct Dyn 2017; 36:3199-3217. [PMID: 28948865 DOI: 10.1080/07391102.2017.1384400] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
HIV-1 integrase is a unique promising component of the viral replication cycle, catalyzing the integration of reverse transcribed viral cDNA into the host cell genome. Generally, IN activity requires both viral as well as a cellular co-factor in the processing replication cycle. Among them, the human lens epithelium-derived growth factor (LEDGF/p75) represented as promising cellular co-factor which supports the viral replication by tethering IN to the chromatin. Due to its major importance in the early steps of HIV replication, the interaction between IN and LEDGF/p75 has become a pleasing target for anti-HIV drug discovery. The present study involves the finding of novel inhibitor based on the information of dimeric CCD of IN in complex with known inhibitor, which were carried out by applying a structure-based virtual screening concept with molecular docking. Additionally, Free binding energy, ADME properties, PAINS analysis, Density Functional Theory, and Enrichment Calculations were performed on selected compounds for getting a best lead molecule. On the basis of these analyses, the current study proposes top 3 compounds: Enamine-Z742267384, Maybridge-HTS02400, and Specs-AE-848/37125099 with acceptable pharmacological properties and enhanced binding affinity to inhibit the interaction between IN and LEDGF/p75. Furthermore, Simulation studies were carried out on these molecules to expose their dynamics behavior and stability. We expect that the findings obtained here could be future therapeutic agents and may provide an outline for the experimental studies to stimulate the innovative strategy for research community.
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Affiliation(s)
- Umesh Panwar
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi 630004 , Tamil Nadu , India
| | - Sanjeev Kumar Singh
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi 630004 , Tamil Nadu , India
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Kim TS, Patel SKS, Selvaraj C, Jung WS, Pan CH, Kang YC, Lee JK. A highly efficient sorbitol dehydrogenase from Gluconobacter oxydans G624 and improvement of its stability through immobilization. Sci Rep 2016; 6:33438. [PMID: 27633501 PMCID: PMC5025769 DOI: 10.1038/srep33438] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/26/2016] [Indexed: 01/14/2023] Open
Abstract
A sorbitol dehydrogenase (GoSLDH) from Gluconobacter oxydans G624 (G. oxydans G624) was expressed in Escherichia coli BL21(DE3)-CodonPlus RIL. The complete 1455-bp codon-optimized gene was amplified, expressed, and thoroughly characterized for the first time. GoSLDH exhibited Km and kcat values of 38.9 mM and 3820 s−1 toward L-sorbitol, respectively. The enzyme exhibited high preference for NADP+ (vs. only 2.5% relative activity with NAD+). GoSLDH sequencing, structure analyses, and biochemical studies, suggested that it belongs to the NADP+-dependent polyol-specific long-chain sorbitol dehydrogenase family. GoSLDH is the first fully characterized SLDH to date, and it is distinguished from other L-sorbose-producing enzymes by its high activity and substrate specificity. Isothermal titration calorimetry showed that the protein binds more strongly to D-sorbitol than other L-sorbose-producing enzymes, and substrate docking analysis confirmed a higher turnover rate. The high oxidation potential of GoSLDH for D-sorbitol was confirmed by cyclovoltametric analysis. Further, stability of GoSLDH significantly improved (up to 13.6-fold) after cross-linking of immobilized enzyme on silica nanoparticles and retained 62.8% residual activity after 10 cycles of reuse. Therefore, immobilized GoSLDH may be useful for L-sorbose production from D-sorbitol.
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Affiliation(s)
- Tae-Su Kim
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea
| | | | - Woo-Suk Jung
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, 25451, Republic of Korea
| | - Cheol-Ho Pan
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, 25451, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea
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Sampath B, Sankaranarayanan K. Glu106 targeted inhibitors of ORAI1 as potential Ca 2+ release-activated Ca 2+ (CRAC) channel blockers - molecular modeling and docking studies. J Recept Signal Transduct Res 2016; 36:572-585. [PMID: 26895524 DOI: 10.3109/10799893.2016.1141956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Calcium release-activated calcium modulator 1(ORAI1) is an integral component of the calcium release-activated calcium channel (CRAC) channel complex and plays a central role in regulating Ca2 + concentrations in T-lymphocytes. It is critical for many physiological processes, including cell-proliferation, cytokine production and activation of the immune system. Loss of ORAI1 function is linked with rheumatoid arthritis (RA) and hence pharmacological blockers of ORAI1 could be potential therapeutic agents for the treatment of RA. In this study, we have used a high-throughput screening approach to inhibit the binding of Ca2+ toward ORAI1 and the interactions are verified through induced fit docking. The results hint that these compounds act by possibly binding with, and thereby blocking Ca2+-binding with ORAI1 (E106). The molecular dynamics (MD) simulations shows strong support toward the hit compounds by showing the ligand potency throughout the simulation timescale of 30 ns. We have thus identified a novel class of highly stable, potential lead compounds that directly bind with the selectivity filter region E106 and block Ca2+ binding on ORAI1. This resulting alteration in the pore geometry of ORAI1 due to the strong blocking mechanism of lead compounds will greatly diminish its function and the downstream activities that result from the same including decreased production of cytokines in autoimmune disorders. This study may lay the foundation for finding novel lead compounds for clinical trials that could positively modulate the course of autoimmune disorders with ORAI1 as its specific target.
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Affiliation(s)
- Bhuvaneshwari Sampath
- a Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University , Chennai , Tamil Nadu , India
| | - Kavitha Sankaranarayanan
- a Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University , Chennai , Tamil Nadu , India
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