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Mandal P, Pradhan SM, Mathew AA, Benny S, Kumar S, Unni AR, S K K. Exploring the effects of vasoactive constituents in large cardamom: implications for the anti-hypertensive effect via eNOS coupling pathway - an in-vitro study in rat endothelial cells. Nat Prod Res 2024:1-7. [PMID: 38742417 DOI: 10.1080/14786419.2024.2351534] [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: 12/13/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
Endothelial dysfunction, linked to reduced eNOS expression and nitric oxide (NO) availability, contributes to cardiovascular diseases (CVDs). Large cardamom exhibits antihypertensive effects by augmenting NO levels and antioxidant activity. To decipher its mechanisms, selected constituents were docked with eNOS-associated target genes such as GTP cyclohydrolase I (GTPCH-1) and (dihydrofolate reductase [DHFR]). Endothelial damage induced by L-NAME and fructose was countered by assessing nitric oxide metabolites (NOx), tetrahydrobipterin (BH4 levels), GCH-I expression and super oxide dismutase (SOD) activity after constituent incubation. Cyanidin-3-O-glucoside and petunidin-3-O-glucoside notably restored impaired vascular markers in both models. These phytoconstituents are likely to activate GCH-BH4-eNOS pathways, upregulating SOD and NO expression, maintaining endothelial integrity. Large cardamom's antihypertensive effects may stem from these components, synergistically enhancing endothelial NO release via the eNOS pathway.
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Affiliation(s)
- Pronay Mandal
- Department of Pharmacology, Amrita School of Pharmacy, Kochi, India
| | | | | | - Sonu Benny
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Kochi, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Kochi, India
| | - Ashok R Unni
- Central Lab Animal Facility, Amrita Institute of Medical Sciences, Kochi, India
| | - Kanthlal S K
- Department of Pharmacology, Amrita School of Pharmacy, Kochi, India
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2
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Manjunath A, Chinmayi GVA, Renganathan S, Chandramohan V, Sabat S. Antimicrobial activity of Geranyl acetate against cell wall synthesis proteins of P. aeruginosa and S. aureus using molecular docking and simulation. J Biomol Struct Dyn 2024; 42:3030-3050. [PMID: 37199273 DOI: 10.1080/07391102.2023.2212060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/01/2023] [Indexed: 05/19/2023]
Abstract
Incidences of Methicillin-Resistant Staphylococcus aureus and Multi-Drug Resistant Pseudomonas aeruginosa causing skin and soft tissue infections are becoming more prevalent due to repeated mutations and changes in the environment. Coriandrum sativum, a well-known Indian herbal medicinal plant, is shown to have antioxidant, antibacterial, and anti-inflammatory activity. This comparative study focuses on the molecular docking (PyRx v0.9.8) of ligand binding domains of WbpE Aminotransferase involved in O-antigen assembly in Pseudomonas aeruginosa (3NU7) and Beta-Lactamase found in Staphylococcus aureus (1BLC) with selected phytocompounds of Coriandrum sativum along with a known binder and a clinical reference drug. This was followed by molecular dynamics simulation studies (GROMACS v2019.4) for the docked complexes (with Geranyl acetate) with the best binding affinities (-23.4304 kJ/mol with Beta-Lactamase and -28.4512 kJ/mol with WbpE Aminotransferase) and maximum hydrogen bonds. Molecular dynamics simulation studies for both the proteins demonstrated that the complex with Geranyl acetate showed stability comparable to the complex with reference drug observed via Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and H-bond analyses. Changes in the secondary structural elements indicated that Geranyl acetate could possibly cause improper functioning of WbpE Aminotransferase leading to disrupted cell wall formation. Further, MM/PBSA analyses showed significant binding affinity of Geranyl acetate with WbpE Aminotransferase and Beta-Lactamase. This study aims to provide rationale for further studies of Coriandrum sativum as an antimicrobial, and to contextualise the results in the current scenario of growing antimicrobial resistance. HIGHLIGHTSPhytoconstituents present in Coriandrum sativum show significant binding affinity to the proteins in Pseudomonas aeruginosa and Staphylococcus aureus.Geranyl acetate exhibited the highest binding affinity with WbpE Aminotransferase involved in O-antigen assembly in Pseudomonas aeruginosa (PDB ID:3NU7) and Beta-Lactamase found in Staphylococcus aureus (PDB ID: 1BLC)Molecular dynamics simulation analyses show that the phytoconstituent, Geranyl acetate has an effect similar to the clinical reference drug, thus exhibiting potential antibacterial activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, India
| | - Sasmita Sabat
- Department of Biotechnology, PES University, Bengaluru, India
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Swargiary A, Daimari M, Swargiary A, Biswas A, Brahma D, Singha H. Identification of phytocompounds as potent inhibitors of sodium/glucose cotransporter-2 leading to diabetes treatment. J Biomol Struct Dyn 2024:1-14. [PMID: 38379332 DOI: 10.1080/07391102.2024.2319674] [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: 09/30/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Type-II diabetes, a major metabolic disorder has threatened the very existence of a healthy life since long ago. Commercially available antidiabetic drugs are known for several adverse effects. The present study attempted to identify potential phytocompounds as inhibitors of sodium/glucose cotransporter-2 (SGLT2), a major protein that helps in glucose re-absorption from renal tubules. A total of 28 phytocompounds were collected based on the literature survey. 3D co-ordinates of phytocompounds were collected from PubChem database. Molecular docking was carried out with SGLT2 protein and the best 3 docking complexes were subjected to molecular dynamics simulation for 100 ns. Free energy changes were also analyzed using MM/PBSA analysis. Phytocompounds were also analyzed for their drug-likeness and ADMET properties. Docking study observed a strong binding affinity of phytocompounds (> -7.0 kcal/mol). More than 10 phytocompounds showed better binding affinity compared to reference drugs. Further analysis of three best docking complexes when analyzed by MD simulation showed better stability and compactness of the complexes compared to reference drug, empagliflozin. MM/PBSA analysis also revealed that van der Waals force and electrostatic energy are the major binding energy involved in the complex formation. Like docking energy, free energy analysis also observed stronger binding energies (ΔGGAS) in SGLT2-phytocompound complexes compared to empagliflozin complex. All the phytocompounds showed drug-likeness and considerable ADMET properties. The study, therefore, suggests that Trifolirhizin-6'-monoacetate, Aspalathin, and Quercetin-3-glucoside could be a possible inhibitor of SGLT2 protein. However, further studies need to be carried out to reveal the exact mode of activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ananta Swargiary
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Manita Daimari
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Arup Swargiary
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Arup Biswas
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Dulur Brahma
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Hiloljyoti Singha
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
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Panda S, Rout M, Mishra S, Turuk J, Pati S, Dehury B. Molecular docking and MD simulations reveal protease inhibitors block the catalytic residues in Prp8 intein of Aspergillus fumigatus: a potential target for antimycotics. J Biomol Struct Dyn 2023:1-16. [PMID: 38149850 DOI: 10.1080/07391102.2023.2298735] [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: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
Abstract
Resistance to azoles and amphotericin B especially in Aspergillus fumigatus is a growing concern towards the treatment of invasive fungal infection. At this critical juncture, intein splicing would be a productive, and innovative target to establish therapies against resistant strains. Intein splicing is the central event for the activation of host protein, essential for the growth and survival of various microorganisms including A. fumigatus. The splicing process is a four-step protease-like nucleophilic cascade. Thus, we hypothesise that protease inhibitors would successfully halt intein splicing and potentially restrict the growth of the aforementioned pathogen. Using Rosetta Fold and molecular dynamics simulations, we modelled Prp8 intein structure; resembling classic intein fold with horse shoe shaped splicing domain. To fully comprehend the active site of Afu Prp8 intein, C1, T62, H65, H818, N819 from intein sequences and S820, the first C-extein residue are selected. Molecular docking shows that two FDA-approved drugs, i.e. Lufotrelvir and Remdesivir triphosphate efficiently interact with Prp8 intein from the assortment of 212 protease inhibitors. MD simulation portrayed that Prp8 undergoes conformational change upon ligand binding, and inferred the molecular recognition and stability of the docked complexes. Per-residue decomposition analysis confirms the importance of F: block R802, V803, and Q807 binding pocket in intein splicing domain towards recognition of inhibitors, along with active site residues through strong hydrogen bonds and hydrophobic contacts. However, in vitro and in vivo assays are required to confirm the inhibitory action on Prp8 intein splicing; which may pave the way for the development of new antifungals for A. fumigatus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Jyotirmayee Turuk
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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Motahar SFS, Tiyoula FN, Motamedi E, Zeinalabedini M, Kavousi K, Ariaeenejad S. Computational Insights into the Selecting Mechanism of α-Amylase Immobilized on Cellulose Nanocrystals: Unveiling the Potential of α-Amylases Immobilized for Efficient Poultry Feed Hydrolysis. Bioconjug Chem 2023; 34:2034-2048. [PMID: 37823388 DOI: 10.1021/acs.bioconjchem.3c00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The selection of an appropriate amylase for hydrolysis poultry feed is crucial for achieving improved digestibility and high-quality feed. Cellulose nanocrystals (CNCs), which are known for their high surface area, provide an excellent platform for enzyme immobilization. Immobilization greatly enhances the operational stability of α-amylases and the efficiency of starch bioconversion in poultry feeds. In this study, we immobilized two metagenome-derived α-amylases, PersiAmy2 and PersiAmy3, on CNCs and employed computational methods to characterize and compare the degradation efficiencies of these enzymes for poultry feed hydrolysis. Experimental in vitro bioconversion assessments were performed to validate the computational outcomes. Molecular docking studies revealed the superior hydrolysis performance of PersiAmy3, which displayed stronger electrostatic interactions with CNCs. Experimental characterization demonstrated the improved performance of both α-amylases after immobilization at high temperatures (80 °C). A similar trend was observed under alkaline conditions, with α-amylase activity reaching 88% within a pH range of 8.0 to 9.0. Both immobilized α-amylases exhibited halotolerance at NaCl concentrations up to 3 M and retained over 50% of their initial activity after 13 use cycles. Notably, PersiAmy3 displayed more remarkable improvements than PersiAmy2 following immobilization, including a significant increase in activity from 65 to 80.73% at 80 °C, an increase in activity to 156.48% at a high salinity of 3 M NaCl, and a longer half-life, indicating greater thermal stability within the range of 60 to 80 °C. These findings were substantiated by the in vitro hydrolysis of poultry feed, where PersiAmy3 generated 53.53 g/L reducing sugars. This comprehensive comparison underscores the utility of computational methods as a faster and more efficient approach for selecting optimal enzymes for poultry feed hydrolysis, thereby providing valuable insights into enhancing feed digestibility and quality.
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Affiliation(s)
- Seyedeh Fatemeh Sadeghian Motahar
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj 31535-1897, Iran
| | - Fereshteh Noroozi Tiyoula
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 14176-14411, Iran
| | - Elaheh Motamedi
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Research and Extension Organization (AREEO), Karaj 55555, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj 31535-1897, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 14176-14411, Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj 31535-1897, Iran
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Ladias C, Papakotoulas P, Papaioannou M, Papanikolaou NA. Overcoming phenotypic switching: targeting protein-protein interactions in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1071-1081. [PMID: 38023990 PMCID: PMC10651353 DOI: 10.37349/etat.2023.00181] [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: 03/08/2023] [Accepted: 08/02/2023] [Indexed: 12/01/2023] Open
Abstract
Alternative protein-protein interactions (PPIs) arising from mutations or post-translational modifications (PTMs), termed phenotypic switching (PS), are critical for the transmission of alternative pathogenic signals and are particularly significant in cancer. In recent years, PPIs have emerged as promising targets for rational drug design, primarily because their high specificity facilitates targeting of disease-related signaling pathways. However, obstacles exist at the molecular level that arise from the properties of the interaction interfaces and the propensity of small molecule drugs to interact with more than one cleft surface. The difficulty in identifying small molecules that act as activators or inhibitors to counteract the biological effects of mutations raises issues that have not been encountered before. For example, small molecules can bind tightly but may not act as drugs or bind to multiple sites (interaction promiscuity). Another reason is the absence of significant clefts on protein surfaces; if a pocket is present, it may be too small, or its geometry may prevent binding. PS, which arises from oncogenic (alternative) signaling, causes drug resistance and forms the basis for the systemic robustness of tumors. In this review, the properties of PPI interfaces relevant to the design and development of targeting drugs are examined. In addition, the interactions between three tyrosine kinase inhibitors (TKIs) employed as drugs are discussed. Finally, potential novel targets of one of these drugs were identified in silico.
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Affiliation(s)
- Christos Ladias
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Epirus, Greece
| | - Pavlos Papakotoulas
- First Department of Clinical Oncology, Theageneio Cancer Hospital, 54639 Thessaloniki, Macedonia, Greece
| | - Maria Papaioannou
- Laboratory of Biological Chemistry, Department of Medicine, Section of Biological Sciences and Preventive Medicine, Aristotle University of Thessaloniki School of Medicine, 54124 Thessaloniki, Macedonia, Greece
| | - Nikolaos A. Papanikolaou
- Laboratory of Biological Chemistry, Department of Medicine, Section of Biological Sciences and Preventive Medicine, Aristotle University of Thessaloniki School of Medicine, 54124 Thessaloniki, Macedonia, Greece
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Wang Z, Ma J, Wang T, Qin C, Hu X, Mosa A, Ling W. Environmental health risks induced by interaction between phthalic acid esters (PAEs) and biological macromolecules: A review. CHEMOSPHERE 2023; 328:138578. [PMID: 37023900 DOI: 10.1016/j.chemosphere.2023.138578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
As a kind of compounds abused in industry productions, phthalic acid esters (PAEs) cause serious problems in natural environment. PAEs pollution has penetrated into environmental media and human food chain. This review consolidates the updated information to assess the occurrence and distribution of PAEs in each transmission section. It is found that micrograms per kilogram of PAEs are exposed to humans through daily diets. After entering the human body, PAEs often undergo the metabolic process of hydrolysis to monoesters phthalates and conjugation process. Unfortunately, in the process of systemic circulation, PAEs will interact with biological macromolecules in vivo under the action of non-covalent binding, which is also the essence of biological toxicity. The interactions usually operate in the following pathways: (a) competitive binding; (b) functional interference; and (c) abnormal signal transduction. While the non-covalent binding forces mainly contain hydrophobic interaction, hydrogen bond, electrostatic interaction, and π interaction. As a typical endocrine disruptor, the health risks of PAEs often start with endocrine disorder, further leading to metabolic disruption, reproductive disorders, and nerve injury. Besides, genotoxicity and carcinogenicity are also attributed to the interaction between PAEs and genetic materials. This review also pointed out that the molecular mechanism study on biological toxicity of PAEs are deficient. Future toxicological research should pay more attention to the intermolecular interactions. This will be beneficial for evaluating and predicting the biological toxicity of pollutants at molecular scale.
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Affiliation(s)
- Zeming Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Junchao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Tingting Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516, Mansoura, Egypt
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Anupama KP, Shilpa O, Antony A, Gurushankara HP. Jatamansinol from Nardostachys jatamansi: a multi-targeted neuroprotective agent for Alzheimer's disease. J Biomol Struct Dyn 2023; 41:200-220. [PMID: 34854369 DOI: 10.1080/07391102.2021.2005681] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial progressive and irreversible neurodegenerative disorder characterized by severe memory impairment and cognitive disability in the middle and old-aged human population. There are no proven drugs for AD treatment and prevention. In Ayurveda, medhya plants are used to prepare Rasayana, and its consumption improves memory and cognition. Nardostachys jatamansi (D.Don) DC is a medhya plant used in traditional medicine to treat neurological disorders, and its unique pyranocoumarins can be a potential drug candidate for AD. Given its traditional claims, this study aims to find the multi-target potential efficacy of the ligands (drug molecules) against the AD from N. jatamansi pyranocoumarins using computational drug discovery techniques. Drug likeliness analysis confirms that pyranocoumarins of N. jatamansi, such as seselin, jatamansinol, jatamansine, jatamansinone, and dihydrojatamansin are probable drug candidates for AD. Molecular docking, molecular dynamic simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) analysis confirm that dihydrojatamansin inhibits acetylcholinesterase (AChE), and jatamansinol inhibits butyrylcholinesterase (BuChE), glycogen synthase kinase 3β (GSK3β), and kelch-like ECH-associating protein 1 (Keap1) AD therapeutic targets. Therefore, this study provides potential multi-target inhibitors that would further validate experimental studies, leading to new treatments for AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kizhakke P Anupama
- Department of Zoology, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, India
| | - Olakkaran Shilpa
- Department of Zoology, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, India
| | - Anet Antony
- Department of Zoology, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, India
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Tsai PW, Tayo LL, Ting JU, Hsieh CY, Lee CJ, Chen CL, Yang HC, Tsai HY, Hsueh CC, Chen BY. Interactive deciphering electron-shuttling characteristics of Coffea arabica leaves and potential bioenergy-steered anti-SARS-CoV-2 RdRp inhibitor via microbial fuel cells. INDUSTRIAL CROPS AND PRODUCTS 2023; 191:115944. [PMID: 36405420 PMCID: PMC9659477 DOI: 10.1016/j.indcrop.2022.115944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 05/29/2023]
Abstract
Due to the pandemics of COVID-19, herbal medicine has recently been explored for possible antiviral treatment and prevention via novel platform of microbial fuel cells. It was revealed that Coffea arabica leaves was very appropriate for anti-COVID-19 drug development. Antioxidant and anti-inflammatory tests exhibited the most promising activities for C. arabica ethanol extracts and drying approaches were implemented on the leaf samples prior to ethanol extraction. Ethanol extracts of C. arabica leaves were applied to bioenergy evaluation via DC-MFCs, clearly revealing that air-dried leaves (CA-A-EtOH) exhibited the highest bioenergy-stimulating capabilities (ca. 2.72 fold of power amplification to the blank). Furthermore, molecular docking analysis was implemented to decipher the potential of C. arabica leaves metabolites. Chlorogenic acid (-6.5 kcal/mol) owned the highest binding affinity with RdRp of SARS-CoV-2, showing a much lower average RMSF value than an apoprotein. This study suggested C. arabica leaves as an encouraging medicinal herb against SARS-CoV-2.
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Key Words
- ADMET,, Absorption-distribution-metabolism-excretion-toxicity
- BBB,, Blood-brain barrier
- Biorefinery
- C. arabica,, Coffea arabica
- CA-40-EtOH,, EtOH extract of C. arabica leaves by 40°C oven-dried
- CA-80-EtOH,, EtOH extract of C. arabica leaves by 80°C oven-dried
- CA-A-EtOH,, EtOH extract of C. arabica leaves by air-dried
- CA-AC,, Acetone extract of C. arabica leaves by 40°C oven-dried
- CA-EA,, Ethyl acetate extract of C. arabica leaves by 40°C oven-dried
- CA-F-EtOH,, EtOH extract of C. arabica leaves by freeze-dried
- CA-H2O,, Water extract of C. arabica leaves by 40°C oven-dried
- CA-HX,, Hexane extract of C. arabica leaves by 40°C oven-dried
- COVID-19
- Chlorogenic acid
- Coffea arabica leaves
- DC-MFCs,, Dual Chamber-Microbial Fuel Cells
- DPPH,, 2,2-diphenyl-1-picrylhydrazyl
- FRAP,, Ferric ion reducing antioxidant power
- MFC,, Microbial fuel cell
- Microbial fuel cells
- QSAR,, Quantitative-structure-activity relationship
- RMSF,, Root-mean-square fluctuation
- RdRp
- RdRp,, RNA-dependent RNA polymerase
- SARS-CoV-2,, Severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Po-Wei Tsai
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan
| | - Lemmuel L Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, 1002 Metro Manila, the Philippines
| | - Jasmine U Ting
- Department of Chemistry, College of Science, De La Salle University, Metro Manila 1004, the Philippines
| | - Cheng-Yang Hsieh
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Chia-Jung Lee
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
- Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Chih-Ling Chen
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan
| | - Hsiao-Chuan Yang
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan 260, Taiwan
| | - Hsing-Yu Tsai
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan 260, Taiwan
| | - Chung-Chuan Hsueh
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan 260, Taiwan
| | - Bor-Yann Chen
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan 260, Taiwan
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Das T, Mukhopadhyay C. Computational studies suggest compounds restoring function of p53 cancer mutants can bind SARS-CoV-2 spike protein. J Biomol Struct Dyn 2022; 41:3368-3381. [PMID: 35333136 DOI: 10.1080/07391102.2022.2048081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
It is reasonable to think that cancer patients undergoing chemotherapy or immunotherapy may have a more aggressive course if they are positive for the novel coronavirus disease. Their compulsive condition requires investigation into effective drugs. We applied computational techniques to a series of compounds known for restoring the function of p53 cancer mutant p53R175H and p53G245S. Two potent inhibitors, 1-(3-chlorophenyl)-3-(1, 3 -thiazol-2-yl) urea (CTU, PubChem NSC321792) with the highest binding affinity -6.92 kcal/mol followed by a thiosemicarbazone compound N'-(1-(Pyridin-2-yl)ethylidene) azetidine - 1 -carbothiohydrazide (NPC, PubChem NSC319726) with -6.75 kcal/mol were subjected to Molecular Dynamics simulation with receptor binding domain (RBD) and compared with control ligand dexamethasone. In particular, CTU adheres to pocket 1 with an average free energy of binding -21.65 ± 2.89 kcal/mol at the RBD - angiotensin-converting enzyme 2 binding region with the highest frequency of amino acid residues after reaching a local equilibrium in 100 ns MD simulation trajectory. A significant enthalpy contribution from the independent simulations unfolds the possibility of dual binding sites for NPC as shifted pocket 1 (-15.59 ± 5.98 kcal/mol) and pocket 2 (-18.90 ± 5.02 kcal/mol). The obtained results for these two compounds are in good agreement with dexamethasone (-18.45 ± 2.42 kcal/mol). Taken together our findings could facilitate the discovery of small molecules that restore the function of p53 cancer mutants newly against COVID-19 in cancer patients.
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Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, Kolkata, India
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Veit-Acosta M, de Azevedo Junior WF. Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery. Curr Med Chem 2021; 29:2438-2455. [PMID: 34365938 DOI: 10.2174/0929867328666210806105810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND CDK2 participates in the control of eukaryotic cell-cycle progression. Due to the great interest in CDK2 for drug development and the relative easiness in crystallizing this enzyme, we have over 400 structural studies focused on this protein target. This structural data is the basis for the development of computational models to estimate CDK2-ligand binding affinity. OBJECTIVE This work focuses on the recent developments in the application of supervised machine learning modeling to develop scoring functions to predict the binding affinity of CDK2. METHOD We employed the structures available at the protein data bank and the ligand information accessed from the BindingDB, Binding MOAD, and PDBbind to evaluate the predictive performance of machine learning techniques combined with physical modeling used to calculate binding affinity. We compared this hybrid methodology with classical scoring functions available in docking programs. RESULTS Our comparative analysis of previously published models indicated that a model created using a combination of a mass-spring system and cross-validated Elastic Net to predict the binding affinity of CDK2-inhibitor complexes outperformed classical scoring functions available in AutoDock4 and AutoDock Vina. CONCLUSION All studies reviewed here suggest that targeted machine learning models are superior to classical scoring functions to calculate binding affinities. Specifically for CDK2, we see that the combination of physical modeling with supervised machine learning techniques exhibits improved predictive performance to calculate the protein-ligand binding affinity. These results find theoretical support in the application of the concept of scoring function space.
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Affiliation(s)
- Martina Veit-Acosta
- Western Michigan University, 1903 Western, Michigan Ave, Kalamazoo, MI 49008. United States
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Karunarathna KHT, Senathilake NHKS, Mewan KM, Weerasena OVDSJ, Perera SACN. In silico structural homology modelling of EST073 motif coding protein of tea Camellia sinensis (L). J Genet Eng Biotechnol 2020; 18:32. [PMID: 32685981 PMCID: PMC7370249 DOI: 10.1186/s43141-020-00038-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/04/2020] [Indexed: 11/17/2022]
Abstract
Background Tea (Camellia sinensis (L). O. Kuntze) is known as the oldest, mild stimulating caffeine containing non-alcoholic beverage. One of the major threats in south Asian tea industry is the blister blight leaf disease (BB), caused by the fungus Exobasidium vexans Masse. SSR DNA marker EST SSR 073 is used as a molecular marker to tag blister blight disease resistance trait of tea. The amino acid sequences were derived from cDNA sequences related to EST SSR 073 of BB susceptible (TRI 2023) and BB resistant (TRI 2043) cultivars. An attempt has been made to understand the structural characteristics and variations of EST SSR 073 locus that may reveal the factors influencing the BB resistance of tea with multiple bioinformatics tools such as ORF finder, ExPasy ProtParam tools, modeler V 9.17, Rampage server, UCSF-Chimera, and HADDOCK docking server. Results The primary, secondary, and tertiary structures of EST SSR 073 coding protein were analyzed using the amino acid sequences of both BB resistant TRI 2043 and BB susceptible TRI 2023 tea cultivars. The coding amino acid sequences of both the cultivars were homologous to photosystem I subunit protein (PsaD I) of Pisum sativum. The predicted 3D structures of proteins were validated and considered as an acceptable overall stereochemical quality. The BB resistant protein showed CT repeat extension and did not involve in topology of the PsaD I subunit. The C terminal truncation of BB resistance caused the formation of hydrogen bonds interacting with PsaD I and other subunits of photosystem I in the modeled three-dimensional protein structure. Conclusions Camellia sinensis EST 073 SSR motif coding protein was identified as the PsaD I subunit of photosystem I. The exact mechanism of PsaD I conferring the resistance for blister blight in tea needs to be further investigated.
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Affiliation(s)
- K H T Karunarathna
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka. .,Current address: Department of biosystems Technology, Faculty of Technology, University of Ruhuna, Matara, Sri Lanka.
| | - N H K S Senathilake
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - K M Mewan
- Department of Biotechnology, Faculty of Agriculture and Plantation Management, Wayamba University of Sri Lanka, Makandura, Gonawila, Sri Lanka
| | - O V D S J Weerasena
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - S A C N Perera
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
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