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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. Molecular insights into the interaction of apo-lactoferrin with the receptor binding domain of the SARS-CoV-2 spike protein: a molecular dynamics simulation study. J Biomol Struct Dyn 2023; 41:7372-7385. [PMID: 36093960 DOI: 10.1080/07391102.2022.2121759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/30/2022] [Indexed: 10/14/2022]
Abstract
LF is a bioactive protein, derived from colostrum and milk that has been found to possess various immunomodulatory, iron chelating, and antimicrobial properties, especially in its apo-form. Recent studies have demonstrated the functionality of LF in attaching to the S proteins of SARS-CoV-2, thereby preventing it from interacting with the ACE-2 receptor. However, the molecular mechanism mediating the process is poorly understood. In this study, molecular docking and MD simulations coupled with free energy calculations were applied to elucidate the key interaction of apo-LF and its N-lobe and C-lobe derivative forms with the RBD of coronavirus S proteins. This has also been extended into evaluating the L452R mutant, which is associated with the delta variant of SARS-CoV-2. The results demonstrate the efficacy of the apo-LF C-lobe in binding to the RBD of both variants, primarily through electrostatic attractions between the acidic residues of the former and the basic residues of each RBD. Furthermore, due to the additional arginine in the L452R variant, the interaction between the C-lobe and the latter is stronger, resulting in a more favourable binding and tightly bound structure. The simulations highlight that the C-lobe, followed by full-length apo-LF can form a multimeric complex with the RBD of SARS-CoV-2, indicating their potential use as novel therapeutics, particularly the cleaved C-lobe of apo-LF to disrupt the S proteins from binding to the host ACE-2 receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kevion K Darmawan
- School of Science, STEM College, RMIT University, Melbourne, Victoria, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Alfred Centre, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jeff G Hughes
- School of Science, STEM College, RMIT University, Melbourne, Victoria, Australia
| | - Darryl M Small
- School of Science, STEM College, RMIT University, Melbourne, Victoria, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, Victoria, Australia
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. Molecular modeling of lactoferrin for food and nutraceutical applications: insights from in silico techniques. Crit Rev Food Sci Nutr 2022; 63:9074-9097. [PMID: 35503258 DOI: 10.1080/10408398.2022.2067824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lactoferrin is a protein, primarily found in milk that has attracted the interest of the food industries due to its health properties. Nevertheless, the instability of lactoferrin has limited its commercial application. Recent studies have focused on encapsulation to enhance the stability of lactoferrin. However, the molecular insights underlying the changes of structural properties of lactoferrin and the interaction with protectants remain poorly understood. Computational approaches have proven useful in understanding the structural properties of molecules and the key binding with other constituents. In this review, comprehensive information on the structure and function of lactoferrin and the binding with various molecules for food purposes are reviewed, with a special emphasis on the use of molecular dynamics simulations. The results demonstrate the application of modeling and simulations to determine key residues of lactoferrin responsible for its stability and interactions with other biomolecular components under various conditions, which are also associated with its functional benefits. These have also been extended into the potential creation of enhanced lactoferrin for commercial purposes. This review provides valuable strategies in designing novel nutraceuticals for food science practitioners and those who have interests in acquiring familiarity with the application of computational modeling for food and health purposes.
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Affiliation(s)
- Kevion K Darmawan
- School of Science, STEM College, RMIT University, Melbourne, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Australia
| | - Jeff G Hughes
- School of Science, STEM College, RMIT University, Melbourne, Australia
| | - Darryl M Small
- School of Science, STEM College, RMIT University, Melbourne, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, Australia
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. Effects of low temperatures on the conformation of apo-lactoferrin and its interactions with α-lactalbumin and β-lactoglobulin: Application of in silico approaches. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. Computational design of de novo nutraceuticals: Effects of spray drying temperatures on the interaction between apo-lactoferrin whey protein complex and the peptidoglycan layer in lactic acid bacteria. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. In silico modelling of apo-lactoferrin under simulated gastric conditions: Structural dynamics, binding with β-lactoglobulin and α-lactalbumin, and functional implications. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Pitsillou E, Liang J, Karagiannis C, Ververis K, Darmawan KK, Ng K, Hung A, Karagiannis TC. Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay. Comput Biol Chem 2020; 89:107408. [PMID: 33137690 PMCID: PMC7583591 DOI: 10.1016/j.compbiolchem.2020.107408] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/12/2020] [Accepted: 10/18/2020] [Indexed: 12/16/2022]
Abstract
Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particular importance. A critical antiviral target is the SARS-CoV-2 main protease (Mpro), and our aim was to identify lead compounds with potential inhibitory effects. We performed an initial molecular docking screen of 300 small molecules, which included phenolic compounds and fatty acids from our OliveNet™ library (224), and an additional group of curated pharmacological and dietary compounds. The prototypical α-ketoamide 13b inhibitor was used as a control to guide selection of the top 30 compounds with respect to binding affinity to the Mpro active site. Further studies and analyses including blind docking were performed to identify hypericin, cyanidin-3-O-glucoside and SRT2104 as potential leads. Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the Mpro active site. An enzyme-linked immunosorbent assay indicated that, albeit, not as potent as the covalent positive control (GC376), our leads inhibited the Mpro with activity in the micromolar range, and an order of effectiveness of hypericin and cyanidin-3-O-glucoside > SRT2104 > SRT1720. Overall, our findings, and those highlighted by others indicate that hypericin and cyanidin-3-O-glucoside are suitable candidates for progress to in vitro and in vivo antiviral studies.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Chris Karagiannis
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia; Food Chemistry, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Katherine Ververis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Kevion K Darmawan
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Ken Ng
- Food Chemistry, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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Liang J, Karagiannis C, Pitsillou E, Darmawan KK, Ng K, Hung A, Karagiannis TC. Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface. Comput Biol Chem 2020; 89:107372. [PMID: 32911432 PMCID: PMC7833639 DOI: 10.1016/j.compbiolchem.2020.107372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) has an important role in the viral life cycle. Inhibition of the active site or dimerization site of Mpro can mitigate activity. Mapping reveals a reactive pocket in the dimerization pocket at the apex of Mpro. Blind docking shows that ligands may preferentially bind at the apex of Mpro. Stable ligand interactions are formed at the active and apex sites of Mpro.
The SARS-CoV-2 virus is causing COVID-19 resulting in an ongoing pandemic with serious health, social, and economic implications. Much research is focused in repurposing or identifying new small molecules which may interact with viral or host-cell molecular targets. An important SARS-CoV-2 target is the main protease (Mpro), and the peptidomimetic α-ketoamides represent prototypical experimental inhibitors. The protease is characterised by the dimerization of two monomers each which contains the catalytic dyad defined by Cys145 and His41 residues (active site). Dimerization yields the functional homodimer. Here, our aim was to investigate small molecules, including lopinavir and ritonavir, α-ketoamide 13b, and ebselen, for their ability to interact with the Mpro. The sirtuin 1 agonist SRT1720 was also used in our analyses. Blind docking to each monomer individually indicated preferential binding of the ligands in the active site. Site-mapping of the dimeric protease indicated a highly reactive pocket in the dimerization region at the domain III apex. Blind docking consistently indicated a strong preference of ligand binding in domain III, away from the active site. Molecular dynamics simulations indicated that ligands docked both to the active site and in the dimerization region at the apex, formed relatively stable interactions. Overall, our findings do not obviate the superior potency with respect to inhibition of protease activity of covalently-linked inhibitors such as α-ketoamide 13b in the Mpro active site. Nevertheless, along with those from others, our findings highlight the importance of further characterisation of the Mpro active site and any potential allosteric sites.
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Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Chris Karagiannis
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia; School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Kevion K Darmawan
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Ken Ng
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. High temperature induced structural changes of apo-lactoferrin and interactions with β-lactoglobulin and α-lactalbumin for potential encapsulation strategies. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Liang J, Pitsillou E, Karagiannis C, Darmawan KK, Ng K, Hung A, Karagiannis TC. Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex. Comput Biol Chem 2020; 87:107292. [PMID: 32485652 PMCID: PMC7253975 DOI: 10.1016/j.compbiolchem.2020.107292] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 12/13/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. In the absence of a vaccine, or an approved effective therapeutic, there is an intense interest in repositioning available drugs or designing small molecule antivirals. In this context, in silico modelling has proven to be an invaluable tool. An important target is the SARS-CoV-2 main protease (Mpro), involved in processing translated viral proteins. Peptidomimetic α-ketoamides represent prototypical inhibitors of Mpro. A recent attempt at designing a compound with enhanced pharmacokinetic properties has resulted in the synthesis and evaluation of the α-ketoamide 13b analogue. Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 Mpro. We included the widely used antibiotic, amoxicillin, for comparison. Our findings indicate that α-ketoamide 13b binds more tightly (predicted GlideScore = -8.7 and -9.2 kcal/mol for protomers A and B, respectively), to the protease active site compared to amoxicillin (-5.0 and -4.8 kcal/mol). Further, molecular dynamics simulations highlight the stability of the interaction of the α-ketoamide 13b ligand with the SARS-CoV-2 Mpro (ΔG = -25.2 and -22.3 kcal/mol for protomers A and B). In contrast, amoxicillin interacts unfavourably with the protease (ΔG = +32.8 kcal/mol for protomer A), with unbinding events observed in several independent simulations. Overall, our findings are consistent with those previously observed, and highlight the need to further explore the α-ketoamides as potential antivirals for this ongoing COVID-19 pandemic.
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Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Chris Karagiannis
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia; School of Agriculture & Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Kevion K Darmawan
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Ken Ng
- School of Agriculture & Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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