Grant/Projek zakończony
In silico investigation of molecular mechanisms of antiviral and antimicrobial activity I
Identyfikator grantu: PT00861
Kierownik projektu: Adam Liwo
Uniwersytet Gdański
Wydział Chemii
Gdańsk
Data otwarcia: 2021-02-01
Data zakończenia: 2023-02-15
Streszczenie projektu
We aim at performing computational studies of properties and interactions of certain biomolecules. Specifically, we plan to investigate the molecular mechanisms of the interaction between the two SARS-CoV-2 proteins ORF6 and Nsp13 with the proteins of the target cells RAE1, RAE1-NUP98, KPNA2, KPNB1, and TBK1. On the computational part, these include development of 3D models of the viral proteins, investigation of their interactions with the cellular targets in order to identify the binding sites, and rational search for molecules capable of blocking the biological activity of ORF6 and Nsp13. The simulations will be guided and validated by laboratory tests. The primary goal of the project is identification of the mechanisms and the corresponding means (existing drugs or new molecules) for unblocking the IFN pathways and reactivating the innate immune response in cells infected by SARS-CoV-2.
As next, we envisage a series of simulations aiming at understanding the biological activity of a natural substance – the Helix aspersa mucus. The identification of the active components in this multicomponent substance is necessary to develop alternative therapies against multi-resistant bacterial strains. In order to study the mechanism of action of certain newly isolated antimicrobial peptides we shall perform simulations of peptide-membrane interactions for selected representative AMPs.
We shall keep (mainly) to all-atom approach, but where suitable, we shall use both all-atom and coarse-grain approaches. The investigated systems range from several hundred thousand to a million atoms and require significant computational resources.
As next, we envisage a series of simulations aiming at understanding the biological activity of a natural substance – the Helix aspersa mucus. The identification of the active components in this multicomponent substance is necessary to develop alternative therapies against multi-resistant bacterial strains. In order to study the mechanism of action of certain newly isolated antimicrobial peptides we shall perform simulations of peptide-membrane interactions for selected representative AMPs.
We shall keep (mainly) to all-atom approach, but where suitable, we shall use both all-atom and coarse-grain approaches. The investigated systems range from several hundred thousand to a million atoms and require significant computational resources.
Publikacje
- N. Ilieva, P. Petkov, E. Lilkova, L. Litov, Probing the membrane-destruction potential of the newly identified peptide aspersin DK10 (DLTLNGLSPK), New biologically active natural peptides, glycopeptides, and proteins Annual Meeting of the National Research Programme “BioActiveMed” (10-13 May 2021, Panagyurishte, Bulgaria & hybrid) 1, (2021) 1
- N. Ilieva, P. Petkov, E. Lilkova, and L. Litov, Computational Study of Helix Aspersa Mucus Peptides in complex with a Model Bacterial Membrane, Large Scale Scientific Computations (LSSC’2021) (7-11 June 2021, Sozopol, Bulgaria & hybrid) 1, (2021) 50
- N. Ilieva, P. Petkov, E. Lilkova, L. Litov , Metadynamics approach to modelling peptide-membrane interactions – a proof-of-concept study, Application of Mathematics in Technical and Natural Sciences (AMiTaNS’21) (24-29 June 2021, Albena, Bulgaria & hybrid) 1, (2021) 1
- N. Ilieva, P. Petkov, E. Lilkova, and L. Litov , Enhanced sampling molecular modeling of peptide-membrane interactions: a case study, Mathematics of Life, MoL’2021 (13-16 September 2021, Hisarya, Bulgaria & online) 1, (2021) 1
- E. Lilkova, P. Petkov, R. Marinova, L. Litov, and N. Ilieva, Observation of charge-dependent membrane-destruction modes in AMP-membrane interactions, C5. International Workshop on Numerical and Symbolic Scientific Computing (20-23 September 2021, Sofia, Bulgaria & online) 1, (2021) 1
- P. Petkov, N. Ilieva, E. Lilkova, L. Litov, Partitioning of Putative Antimicrobial Peptides into a Model Bacterial Membrane: a Metadynamics Approach., Studies in Computational Intelligence (Springer, accepted 2022) (print) 037, (2022) 1860-9503
- Y. Cheng, X. Peng, P. Petkov, N. Ilieva, Impact of the grafting topology on the geometry and dynamics of the prospective Parkinson inhibitor MCoCP4, Numerical Solutions of Fractional Differential Equations and Applications (Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, 2022) (eBook) (open access) 1, (2022) 23-16
- P. Petkov, N. Ilieva, E. Lilkova, L. Litov, Orchestrated membrane penetrations as a means of studying peptide-membrane specific affinity, Numerical Solutions of Fractional Differential Equations and Applications (Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, 2022) (ebook) 1, (2022) 52-54
- P. Petkov, E. Lilkova, L. Litov, N. Ilieva, Charge dependence of the membrane destruction modes of linear antimicrobial peptides: a case study , 16th Annual Meeting of the Bulgarian Section of SIAM (21-23 December 2021, Sofia & online), Book of Abstracts 1, (2021) 52
- Y. Cheng, X. Peng, P. Petkov, N. Ilieva, Impact of the grafting topology on the geometry and dynamics of the prospective Parkinson inhibitor MCoCP4, Second International Workshop Numerical Solution of Fractional Differential Equations and Applications (NSFDE&A), (June 5 - 10, 2022, Sozopol, Bulgaria) 1, (2022) 1
- P. Petkov, N. Ilieva, E. Lilkova, L. Litov, Orchestrated membrane penetrations as a means of studying peptide-membrane specific affinity, Second International Workshop Numerical Solution of Fractional Differential Equations and Applications (NSFDE&A), (June 5 - 10, 2022, Sozopol, Bulgaria) 1, (2022) 1
- N. Ilieva, P. Petkov, E. Lilkova, L. Litov, Investigation of the specific membrane activity of peptides via orchestrated membrane translocation, Third National Conference on Low-Toxic Bioactive Substances for Precision Medicine (BioActiveMed) (13-15 June 2022, Kyustendil, Bulgaria) 1, (2022) 1
- P. Petkov, E. Lilkova, L. Litov, N. Ilieva, In silico studies on the peptide-membrane-interaction energetics, 10th Conference on Numerical Methods and Applications (NM&A’22) (August 22 - 26, 2022, Borovets, Bulgaria) 1, (2022) 1
- E. Lilkova, P. Petkov, R. Marinova, L. Litov, and N. Ilieva, Self-Association of Antimicrobial Peptides in Mono- and Multicomponent Solutions: a Computational Study, 11th Congress of Balkan Physicists Union (28 August – 1 September 2022, Belgrade, Serbia) 1, (2022) 223-224
- Peicho Petkov, Rositsa Marinova, Elena Lilkova, Nevena Ilieva, Leandar Litov, Self-Association Evidence for Antimicrobial Peptides via Long-Scale MD Simulations: a Case Study, The 2nd International Electronic Conference on Biomolecules: Biomacromolecules and the Modern World Challenges (11-15 November 2022, online) 1, (2022) 1
- E. Lilkova, P. Petkov, N. Ilieva, L. Litov, Concentration-Dependant Behaviour of AMPs in Solution, 17th Annual Meeting of the Bulgarian Section of SIAM (20-22 December 2022, Sofia & online) – with international participation 1, (2022) 25
- T. Nedeva, M. Rangelov, N. Hristova, E. Lilkova, P. Petkov, N. Ilieva, L. Litov, Modeling the Interaction of SARS-COV-2 NSP13 with Human TBK1, 17th Annual Meeting of the Bulgarian Section of SIAM (20-22 December 2022, Sofia & online) – with international participation 1, (2022) 29