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Article ; Online: A repository of COVID-19 related molecular dynamics simulations and utilisation in the context of nsp10-nsp16 antivirals.

Liang, Julia J / Pitsillou, Eleni / Hung, Andrew / Karagiannis, Tom C

Journal of molecular graphics & modelling

2023 Volume 126, Page(s) 108666

Abstract: The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of establishing systems and infrastructure to develop vaccines, antiviral drugs, and therapeutic antibodies against emerging pathogens. Typical drug discovery processes involve ... ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of establishing systems and infrastructure to develop vaccines, antiviral drugs, and therapeutic antibodies against emerging pathogens. Typical drug discovery processes involve targeting suitable proteins to effect pathogen replication or to attenuate host responses, by examining either large chemical databases or protein-protein interactions. Following initial screens, molecular dynamics (MD) simulations are critical for gaining further insight into molecular interactions. During the COVID-19 pandemic, many research groups made their simulations widely available, as highlighted by the comprehensive D.E. Shaw Research trajectory database. To investigate protein target sites and evaluate potential lead compounds, we performed over 300 MD simulations relating to COVID-19. We organised our simulations into a repository, which is publicly available at https://epimedlab.org/trajectories/. The trajectories cover a large part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome, and the majority of our MD simulations focused on the identification of potential antivirals. For example, we focused on the S-adenosyl-l-methionine binding site of the nsp10-nsp16 complex, a critical component of viral replication, revealing verbascoside as a potential lead. Moreover, we utilised MD trajectories to explore the interface between the spike protein receptor binding domain and human angiotensin-converting enzyme 2 receptor, with the ultimate aim being investigation of new variants in real-time. Overall, MD simulations are a critical component of the in silico drug discovery process and as highlighted throughout the pandemic, data sharing enables accelerated progress. We have organised our extensive collection of COVID-19 related MD trajectories into an easily accessible repository.
MeSH term(s)	Humans ; COVID-19 ; Molecular Dynamics Simulation ; SARS-CoV-2 ; Pandemics ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Antiviral Agents/chemistry
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2023-11-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2023.108666
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Article ; Online: Identification of dietary compounds that interact with the circadian clock machinery: Molecular docking and structural similarity analysis.

Pitsillou, Eleni / Liang, Julia J / Beh, Raymond C / Hung, Andrew / Karagiannis, Tom C

Journal of molecular graphics & modelling

2023 Volume 123, Page(s) 108529

Abstract: The molecular clock is vital for regulating circadian rhythms in various physiological processes, and its dysregulation is associated with multiple diseases. As such, the use of small molecule modulators to regulate the molecular clock presents a ... ...

Abstract	The molecular clock is vital for regulating circadian rhythms in various physiological processes, and its dysregulation is associated with multiple diseases. As such, the use of small molecule modulators to regulate the molecular clock presents a promising therapeutic approach. In this study, we generated a homology model of the human circadian locomotor output cycles kaput (CLOCK) protein to evaluate its ligand binding sites. Using molecular docking, we obtained further insights into the binding mode of the control compound CLK8 and explored a selection of dietary compounds. Our investigation of dietary compounds was guided by their potential interactions with the retinoic acid-related orphan receptors RORα/γ, which are involved in circadian regulation. Through the molecular similarity and docking analyses, we identified oleanolic acid demethyl, 3-epi-lupeol, and taraxasterol as potential ROR-interacting compounds. These compounds may exert therapeutic effects through their modulation of RORα/γ activity and subsequently influence the molecular clock. Overall, our study highlights the potential of small molecule modulators in regulating the molecular clock and the importance of exploring dietary compounds as a source of such modulators. Our findings also provide insights into the binding mechanisms of CLK8 and shed light on potential compounds that can interact with RORs to regulate the molecular clock. Future investigations could focus on validating the efficacy of these compounds in modulating the molecular clock and their potential use as therapeutic agents.
MeSH term(s)	Humans ; Circadian Clocks/physiology ; Molecular Docking Simulation ; Circadian Rhythm/physiology ; Binding Sites ; Ligands
Chemical Substances	Ligands
Language	English
Publishing date	2023-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2023.108529
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Article ; Online: Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity.

Pitsillou, Eleni / Yu, Yiping / Beh, Raymond C / Liang, Julia J / Hung, Andrew / Karagiannis, Tom C

Clinical and experimental medicine

2023 Volume 23, Issue 7, Page(s) 3277–3298

Abstract: Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health ... ...

Abstract	Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Pandemics ; Virulence ; Disease Management ; Vaccines
Chemical Substances	spike protein, SARS-CoV-2 ; Vaccines
Language	English
Publishing date	2023-08-24
Publishing country	Italy
Document type	Journal Article ; Review
ZDB-ID	2053018-3
ISSN	1591-9528 ; 1591-8890
ISSN (online)	1591-9528
ISSN	1591-8890
DOI	10.1007/s10238-023-01168-0
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Zs.A 5481: Show issues

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Article ; Online: The SARS-CoV-2 helicase as a target for antiviral therapy: Identification of potential small molecule inhibitors by in silico modelling.

Pitsillou, Eleni / Liang, Julia / Hung, Andrew / Karagiannis, Tom C

Journal of molecular graphics & modelling

2022 Volume 114, Page(s) 108193

Abstract: ... hepatitis C NS3 helicase, and mouse Dna2 nuclease-helicase were used for comparison. As expected, sequence ...

Abstract	Although vaccines that provide protection against severe illness from coronavirus disease (COVID-19) have been made available, emerging variant strains of severe acute respiratory syndrome 2 coronavirus 2 (SARS-CoV-2) are of concern. A different research direction involves investigation of antiviral therapeutics. In addition to structural proteins, the SARS-CoV-2 non-structural proteins are of interest and this includes the helicase (nsp13). In this study, an initial screen of 300 ligands was performed to identify potential inhibitors of the SARS-CoV-2 nsp13 examining the nucleoside triphosphatase site (NTPase activity) as the target region. The antiviral activity of polyphenols has been previously reported in the literature and as a result, the phenolic compounds and fatty acids from the OliveNet™ library were utilised. Synthetic compounds with antimicrobial and anti-inflammatory properties were also selected. The structures of the SARS-CoV and MERS-CoV helicases, as well as the human RECQ-like DNA helicase, DHX9 helicase, PcrA helicase, hepatitis C NS3 helicase, and mouse Dna2 nuclease-helicase were used for comparison. As expected, sequence and structural homology between the various species was evident. A number of broad-spectrum and well-known inhibitors interacted with the NTPase active site highlighting the need to potentially identify more specific inhibitors for SARS-CoV-2. Acetylcysteine, clavulanic acid and homovanillic acid were identified as potential lead compounds for the SARS-CoV-2 helicase. Molecular dynamics simulations were performed with the leads bound to the SARS-CoV-2 helicase for 200 ns in triplicate, with favourable binding free energies to the NTPase site. Given their availability, further exploration of their potential inhibitory activity could be considered.
MeSH term(s)	Animals ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; DNA Helicases/metabolism ; Humans ; Mice ; Molecular Dynamics Simulation ; Nucleoside-Triphosphatase/metabolism ; RNA Helicases/chemistry ; RNA Helicases/metabolism ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Nucleoside-Triphosphatase (EC 3.6.1.15) ; DNA Helicases (EC 3.6.4.-) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2022-04-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2022.108193
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Article: Inhibition of interferon-stimulated gene 15 and lysine 48-linked ubiquitin binding to the SARS-CoV-2 papain-like protease by small molecules:

Pitsillou, Eleni / Liang, Julia / Hung, Andrew / Karagiannis, Tom C

Chemical physics letters

2021 Volume 771, Page(s) 138468

Abstract: The SARS-CoV-2 papain-like protease ( ... ...

Abstract	The SARS-CoV-2 papain-like protease (PL
Language	English
Publishing date	2021-03-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1466293-0
ISSN	0009-2614
ISSN	0009-2614
DOI	10.1016/j.cplett.2021.138468
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Article ; Online: Identification of Potential Modulators of a Pathogenic G Protein-Gated Inwardly Rectifying K

Pitsillou, Eleni / Logothetis, Alexander N O / Liang, Julia J / El-Osta, Assam / Hung, Andrew / AbuMaziad, Asmaa S / Karagiannis, Tom C

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 24

Abstract: Genetic abnormalities have been associated with primary aldosteronism, a major cause of secondary hypertension. This includes mutations in ... ...

Abstract	Genetic abnormalities have been associated with primary aldosteronism, a major cause of secondary hypertension. This includes mutations in the
MeSH term(s)	Humans ; G Protein-Coupled Inwardly-Rectifying Potassium Channels/genetics ; G Protein-Coupled Inwardly-Rectifying Potassium Channels/metabolism ; Ligands ; Molecular Docking Simulation ; GTP-Binding Proteins/metabolism ; Hypertension ; Peptides/metabolism ; Drug Discovery
Chemical Substances	G Protein-Coupled Inwardly-Rectifying Potassium Channels ; Ligands ; GTP-Binding Proteins (EC 3.6.1.-) ; Peptides ; KCNJ5 protein, human
Language	English
Publishing date	2023-12-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28247946
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Article: The timeless influence of Hippocratic ideals on diet, salicytates and personalized medicine.

Karagiannis, Tom C

Hellenic journal of nuclear medicine

2014 Volume 17, Issue 1, Page(s) 2–6

Abstract: ... development and c) personalized medicine. ...

Abstract	At a time when superstition and deities were thought to be responsible for health and disease, Hippocrates of Kos emerged as a rational thinker assigning disease to natural causes. His insights, which principally arose from what may be considered almost compulsive examination and comparison, formed the basis of Hippocratic Medicine. There are still unresolved questions regarding the authenticity of the approximately 70 works shaping the Hippocratic Corpus. Assigning authorship precisely presents difficulties and given that the various treatises in the collection appear to span a period of between 100 and 300 years, it is clear that they may not be ascribed to a single author. Ancient commentaries, including translation and annotation by the Hellenic physician Galen and more recently by Emile Littré have helped preserve and structure our knowledge of Hippocratic ideals. Further, a large school of contemporary scholars are constantly refining our understanding. Despite the controversies and uncertainties, the underlying themes of Hippocrates' influence on medicine which involve meticulous observation, comparison, prognosis and prediction are evident. Importantly, the Hippocratic Oath remains a masterpiece of medical morals and ethics, analogous forms of which are still used today. Indeed, the Hippocratic Corpus teaches timeless concepts which do not only relate to medical thought and methodology but also to the more gentle aspects of the art. In this essay Hippocratic observations are considered in relation to three important matters preoccupying modern medicine: a) nutrition, b) drug development and c) personalized medicine.
Language	English
Publishing date	2014-01
Publishing country	Greece
Document type	Editorial
ZDB-ID	2186026-9
ISSN	1790-5427 ; 1108-1430
ISSN	1790-5427 ; 1108-1430
DOI	10.1967/s0024499100110
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Zs.A 6058: Show issues

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Article ; Online: 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.

Darmawan, Kevion K / Karagiannis, Tom C / Hughes, Jeff G / Small, Darryl M / Hung, Andrew

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 15, Page(s) 7372–7385

Abstract: ... applied to elucidate the key interaction of apo-LF and its N-lobe and C-lobe derivative forms with the RBD ... with the delta variant of SARS-CoV-2. The results demonstrate the efficacy of the apo-LF C-lobe in binding ... variant, the interaction between the C-lobe and the latter is stronger, resulting in a more favourable ...

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.
Language	English
Publishing date	2022-09-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2121759
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Zs.A 2093: Show issues

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Article ; Online: Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain.

Pitsillou, Eleni / Liang, Julia J / Beh, Raymond C / Hung, Andrew / Karagiannis, Tom C

Computers in biology and medicine

2022 Volume 149, Page(s) 106035

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 variant (Omicron), represents a significant deviation in genetic makeup and function compared to previous variants. Following the BA.1 sublineage, the BA.2 and BA.3 Omicron ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 variant (Omicron), represents a significant deviation in genetic makeup and function compared to previous variants. Following the BA.1 sublineage, the BA.2 and BA.3 Omicron subvariants became dominant, and currently the BA.4 and BA.5, which are quite distinct variants, have emerged. Using molecular dynamics simulations, we investigated the binding characteristics of the Delta and Omicron (BA.1) variants in comparison to wild-type (WT) at the interface of the spike protein receptor binding domain (RBD) and human angiotensin converting enzyme-2 (ACE2) ectodomain. The primary aim was to compare our molecular modelling systems with previously published observations, to determine the robustness of our approach for rapid prediction of emerging future variants. Delta and Omicron were found to bind to ACE2 with similar affinities (-39.4 and -43.3 kcal/mol, respectively) and stronger than WT (-33.5 kcal/mol). In line with previously published observations, the energy contributions of the non-mutated residues at the interface were largely retained between WT and the variants, with F456, F486, and Y489 having the strongest energy contributions to ACE2 binding. Further, residues N440K, Q498R, and N501Y were predicted to be energetically favourable in Omicron. In contrast to Omicron, which had the E484A and K417N mutations, intermolecular bonds were detected for the residue pairs E484:K31 and K417:D30 in WT and Delta, in accordance with previously published findings. Overall, our simplified molecular modelling approach represents a step towards predictive model systems for rapidly analysing arising variants of concern.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/genetics ; Humans ; Molecular Dynamics Simulation ; Mutation ; Peptidyl-Dipeptidase A/genetics ; Peptidyl-Dipeptidase A/metabolism ; Protein Binding ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-08-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.106035
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Article ; Online: Molecular modeling of lactoferrin for food and nutraceutical applications: insights from in silico techniques

Darmawan, Kevion K. / Karagiannis, Tom C. / Hughes, Jeff G. / Small, Darryl M. / Hung, Andrew

Critical Reviews in Food Science and Nutrition. 2023 Nov. 6, v. 63, no. 28 p.9074-9097

2023

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 ... ...

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.
Keywords	computer simulation ; dietary supplements ; encapsulation ; lactoferrin ; milk ; molecular dynamics ; Antimicrobials ; bioactive proteins ; functional foods ; whey proteins
Language	English
Dates of publication	2023-1106
Size	p. 9074-9097.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	1037504-1
ISSN	1549-7852 ; 1040-8398
ISSN (online)	1549-7852
ISSN	1040-8398
DOI	10.1080/10408398.2022.2067824
Database	NAL-Catalogue (AGRICOLA)

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