Laboratory of Computational Modeling of Biological Processes

Karen Nazaryan

Head of the laboratory, DSc

Laboratory members

Grigor Arakelov, PhD
Senior researcher
Vahram Arakelov, PhD
Arsen Sargsyan
PhD student
Nelli Muradyan
PhD student
Adrine Paronyan
PhD student
Tigran Tsaturyan
Senior laboratory assistant

General information

The Laboratory of Computational Modeling of Biological Processes was founded in 2007 based on the Laboratory of
Organ-Specific Proteins. The main priority of the laboratory is the application of modern methods of structural
bioinformatics and computational biology for the modeling and in silico analysis of the processes of protein-protein,
protein-ligand interaction, and its regulation. The study of the tubulin-cytostatic drug interaction in the laboratory had
important practical implications for elucidating the molecular mechanisms of genetically determined FMF (Familial
Mediterranean Fever). Investigation of tubulin-cytostatics interaction has severe consequences in terms of practical
use in the case of genetically determined FMF treatment. Recent research has focused on the detailed in silico
analysis of different domains and motifs of the pyrin protein, mutations of which are responsible for the
manifestation of FMF by/with apoptosis factors. It revealed new ways to control FMF development.
Research is also being carried out to model the tertiary structure of proteins that are important in the development of
various viral diseases (African swine fever virus, SARS-CoV-2 virus) and cancer, interactions with other proteins,
and molecular mechanisms of disease.
Our laboratory has developed its workflow for carrying out experiments, in which almost all structural bioinformatics
approaches are applied, including the drug design tools. The laboratory is also engaged in improving the work of
algorithms widely used in computer experiments. In the research process, the own computer cluster and the
capabilities of internationally available supercomputers are used.

Current Research Projects

  • «In silico screening and de novo design of the 14-3-3 proteins interaction network modulators: new opportunities
    for drug discovery in cancer, autoinflammatory and viral diseases», SC RA / 21AG-1F057
    «De novo design and in silico screening of SARS-CoV-2 nucleocapsid protein and 14-3-3 isoforms interaction
    modulators», SC RA / 22AA-1F026

Selected publications

  1. Grigoryan R, Arabyan E, 1. Matevosyan M, Harutyunyan V, Abelyan N, Khachatryan H, Tirosyan I, Gabrielyan Y, Sahakyan V, Gevorgyan
    S, Arakelov V, Arakelov G, Zakaryan H. Design of new chemical entities targeting both native and H275Y
    mutant influenza a virus by deep reinforcement learning. Journal of Biomolecular Structure and Dynamics. 2022
    Dec 21:1-15. doi: 10.1080/07391102.2022.2158936
    2. Al-Sanea MM, Chilingaryan G, Abelyan N, Arakelov G, Sahakyan H, Arakelov VG, Nazaryan K, Hussein S,
    Alazmi GM, Alsharari HE, Al-Faraj WM, Alruwaili FS, Albilasi NQ, Alsharari TS, Alsaleh AAS, Alazmi TM,
    Almalki AH, Alotaibi NH, Abdelgawad MA. Identification of non-classical hCA XII inhibitors using
    combination of computational approaches for drug design and discovery. Sci Rep. 2021 Jul 30;11(1):15516. doi:
    3. Sahakyan H, Abelyan N, Arakelov V, Arakelov G, Nazaryan K. In silico study of colchicine resistance molecular
    mechanisms caused by tubulin structural polymorphism. PLoS One. 2019 Aug 23;14(8):e0221532. doi:
    4. Arakelov G, Arakelov V, Nazaryan K. Complex formation dynamics of native and mutated pyrin's B30.2 domain
    with caspase-1. Proteins. 2018 Jun;86(6):676-683. doi: 10.1002/prot.25494
    5. Arakelov GG, Osipov OV, Nazaryan KB. [Influence of M680I and M694V mutations on pyrin's domain B30.2
    tertiary structure and it's complex formation ability with caspase-1]. Mol Biol (Mosk). 2015 Sep-Oct;49(5):826-
    31. Russian. doi: 10.7868/S002689841505002X