Összes szerző

Hoffka Gyula

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Hoffka Gyula
Crystallographic and molecular dynamics simulations shed light on the self-inactivated conformation of the Venezuelan equine encephalitis virus (VEEV) protease

Aug 29 - kedd

15:30 – 17:00

I. Poszterszekció

P12

Crystallographic and molecular dynamics simulations shed light on the self-inactivated conformation of the Venezuelan equine encephalitis virus (VEEV) protease

Gyula Hoffka1,2, George T. Lountos3, József Tőzsér1 and János András Mótyán1

1 University of Debrecen, Faculty of Medicine, Department of Biochemistry and Molecular Biology, Laboratory of Retroviral Biochemistry

2 University of Debrecen, Doctoral School of Molecular Cell and Immune Biology

3 Frederick National Laboratory for Cancer Research, Basic Science Program

The application of computational simulations in molecular biology allows us to examine a wide range of properties of enzymes, which would otherwise be challenging using experimental methods. Molecular dynamics are exceptionally useful to study conformational landscapes, substrate binding patterns, as well as interaction networks.

The Venezuelan equine encephalitis virus (VEEV) is responsible for causing mild to severe disease in both humans and livestock. The non-structural protein 2 protease (nsP2pro) of VEEV is considered as a drug target due to its crucial role in the viral life-cycle. Therefore, investigation of this viral protein may provide valuable information for structure-based drug design.

We aimed to study the structure of VEEV nsP2pro using both in vitro and in silico approaches. The structure, containing the wild-type N475 N-terminal residue at the active site, was determined experimentally at high resolution (1.46 Å), using X-ray crystallography [1]. The protein exhibited an unexpected conformation wherein the N-terminus mimics substrate binding. This self-inactivated conformation was previously observed only for a N475A mutant enzyme.

To compare the active and inactive conformers, we have used the Amber16 software for molecular dynamics simulations. We investigated the dynamic hydrogen bond networks at the active site, and compared the differences between the dynamic properties of the active and self-inactivated conformers as well as between the N475 and A475 containing variants. The comparison sheds light on the interactions that are crucial to the stabilization of the conformers.

Project no. TKP2021-EGA-20 (Biotechnology) has been implemented with the support provided from the National Research, Development and Innovation Fund of Hungary, financed under the TKP2021-EGA funding scheme. We acknowledge KIFÜ for awarding us access to resource based in Hungary.

[1] Hoffka G, Lounto GT, Needle D, Wlodawer A, Waugh DS, Tőzsér J, Mótyán JA (2023) J Mol Biol 435:168012

Hoffka Gyula
Multiscale computational study on the binding of nirmatrelvir to SARS-CoV-2 main protease: possible pathways to resistance

Aug 29 - kedd

10:00 – 10:15

Molekuláris biofizika

E06

Multiscale computational study on the binding of nirmatrelvir to SARS-CoV-2 main protease: possible pathways to resistance

Gyula Hoffka1,2, Mohamed Mahdi1, József Tőzsér1 and János András Mótyán1

1 University of Debrecen, Faculty of Medicine, Department of Biochemistry and Molecular Biology, Laboratory of Retroviral Biochemistry

2 University of Debrecen, Doctoral School of Molecular Cell and Immune Biology

The pandemic caused by SARS-CoV-2 has resulted in millions of infections worldwide. Multiple vaccination strategies are available, but the number of the antivirals which are specific for SARS-CoV-2 is still limited. The Paxlovid is an antiviral combination that has been developed by Pfizer to treat non-hospitalized COVID-19 patients. It contains nirmatrelvir, a covalent inhibitor of the SARS-CoV-2 main protease (Mpro). Similar to the SARS-CoV-2 spike protein, the Mpro is also prone to mutations, which mutations may potentially interfere with binding of ligands, including nirmatrelvir, leading to the emergence of resistance.

In order to study the structural background of enzyme-inhibitor interactions, we examined the non-covalent interactions, as well as the reaction mechanism of SARS-CoV-2 Mpro with a peptide substrate and nirmatrelvir inhibitor. The interactions between the enzyme and the peptide substrate or nirmatrelvir were compared based on multiple crystal structures [1]. We mapped the crucial non-covalent interactions by applying molecular dynamics simulations for structural analyses. Mechanism of substrate cleavage and nirmatrelvir binding at atomic level were investigated by applying hybrid QM/MM ONIOM method. Previously described nirmatrelvir-resistant SARS-CoV-2 Mpro variants were also investigated to study the mechanism of resistance.

Our results contribute to a better understanding of the molecular mechanism underlying the substrate cleavage and nirmatrelvir binding. Based on a comprehensive analysis of our computational simulations, we propose how individual mutations of the active site may contribute to resistance development.

This work was supported in part by TKP2021-EGA-20 (Biotechnology) and POST-COVID2021-16 projects. We acknowledge KIFÜ for awarding us access to resource based in Hungary.

[1] Mótyán JA, Mahdi M, Hoffka G, Tőzsér J (2022) Int J Mol Sci 23:3507