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The role of Tyr102 residue in the functioning of bacterial NAD

Autor: А V, Popinako, А А, Pometun, D K, Nilov, D V, Dibrova, V V, Khrustalev, T A, Khrustaleva, T S, Iurchenko, А Yu, Nikolaeva, V K, Švedas, K М, Boyko, V I, Tishkov, V О, Popov

Publikováno v: Biochemical and biophysical research communications. 616

Once you have missed the first button …, you'll never manage to button up Johann Wolfgang von Goethe Formate oxidation is a final step of methanol oxidation in methylotrophic prokaryotes and is important for detoxification of formate in other organ

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::bc6cbe532bbbcad491c070e63d945fd6
https://pubmed.ncbi.nlm.nih.gov/35667288

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vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses

Autor: D. K. Nilov, Dmitry A. Suplatov, I. V. Gushchina, Aleksandra M. Polenova, Vytas K. Švedas

Publikováno v: Journal of Chemical Information and Modeling. 60:3692-3696

The ability of ligands to form crucial interactions with a protein target, characteristic for the substrate and/or inhibitors, could be considered a structural criterion for identifying potent binders among docked compounds. Structural filtration of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f311a8890e5d62528b0ab600386118e8
https://doi.org/10.1021/acs.jcim.0c00303

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Mechanisms of Nucleosome Reorganization by PARP1

Autor: Sohail Akhtar, John M. Pascal, N. S. Gerasimova, Elena Kotova, Mikhail P. Kirpichnikov, D. K. Nilov, Marie-France Langelier, Sergey Pushkarev, N. V. Maluchenko, Alexey V. Feofanov, Vasily M. Studitsky

Publikováno v: International Journal of Molecular Sciences, Vol 22, Iss 12127, p 12127 (2021)
International Journal of Molecular Sciences
Volume 22
Issue 22

Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair, chromatin organization and transcription. During transcription initiation, PARP1 interacts with gene promoters where it binds to nucleosomes, replaces linker histone H1 and pa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f29d93424ff27c62d53d55374d23165
https://www.mdpi.com/1422-0067/22/22/12127

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Design, Synthesis, and Molecular Docking Study of New Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors Combining Resin Acids and Adamantane Moieties

Autor: Vytas K. Švedas, Olga I. Lavrik, Vasily N. Konev, Tatiana B. Khlebnikova, Konstantin Ponomarev, E. V. Suslov, Olga I. Yarovaya, Sergey V. Cheresiz, Nariman F. Salakhutdinov, Amirhossein Azimirad, Alexandra L. Zakharenko, Andrey G. Pokrovsky, Irina A. Chernyshova, Evgenii S. Mozhaytsev, D. K. Nilov, Kseniya S. Kovaleva

Publikováno v: Pharmaceuticals
Volume 14
Issue 5
Pharmaceuticals, Vol 14, Iss 422, p 422 (2021)

In this paper, a series of novel abietyl and dehydroabietyl ureas, thioureas, amides, and thioamides bearing adamantane moieties were designed, synthesized, and evaluated for their inhibitory activities against tyrosil-DNA-phosphodiesterase 1 (TDP1).

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::faeb9a98ba8a2b0e4fec8854d422f6fc

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Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins

Autor: Garri Manasaryan, D. K. Nilov, Vytas K. Švedas, Sergey Pushkarev, A. N. Kuimov, Dmitry A. Suplatov, Viktor Drobot

Publikováno v: Cancers, Vol 13, Iss 1201, p 1201 (2021)
Cancers
Volume 13
Issue 6

Simple Summary The PARP family consists of 17 proteins, and some of them are responsible for cancer cells’ viability. Much attention is therefore given to the search for chemical compounds with the ability to suppress distinct PARP family members (

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::df21e4be9bed3b8c32c3a715197a0148
https://www.mdpi.com/2072-6694/13/6/1201

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Requirement for Serine-384 in Caspase-2 processing and activity

Autor: D. K. Nilov, Aleksandra Yu Egorshina, Anna S. Gorbunova, Gelina S. Kopeina, Maria V Turkina, Boris Zhivotovsky, Pavel I. Volik, Svetlana Iu Iarovenko, Alexey V. Zamaraev

Publikováno v: Cell Death & Disease
Cell Death and Disease, Vol 11, Iss 10, Pp 1-13 (2020)

Caspase-2 is a unique and conservative cysteine protease which plays an important role in several cellular processes including apoptotic cell death. Although the molecular mechanisms of its activation remain largely unclear, a major role belongs to t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ca3b4e8af8ffa847e3c57cef212fa46c
https://pubmed.ncbi.nlm.nih.gov/33011746

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Modeling of the Enzyme-Substrate Complexes of Human Poly(ADP-Ribose) Polymerase 1

Autor: D. K. Nilov, Sergey Pushkarev, G. A. Manasaryan, Vytas K. Švedas, I. V. Gushchina, K. I. Kirsanov

Publikováno v: Biochemistry. Biokhimiia. 85(1)

Poly(ADP-ribose) polymerase 1 (PARP-1) is a key DNA repair enzyme and an important target in cancer treatment. Conventional methods of studying the reaction mechanism of PARP-1 have limitations because of the complex structure of PARP-1 substrates; h

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8a93f4269292dff89a1ae5d3164f131a
https://pubmed.ncbi.nlm.nih.gov/32079521

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Molecular Mechanisms of PARP-1 Inhibitor 7-Methylguanine

Autor: Tatyana A. Kurgina, N. S. Gerasimova, Mikhail A. Kutuzov, N. V. Maluchenko, Vasily M. Studitsky, Alexandra Lys, Olga I. Lavrik, Sergey Pushkarev, Alexey V. Feofanov, Vytas K. Švedas, D. K. Nilov

Publikováno v: International Journal of Molecular Sciences
International Journal of Molecular Sciences, Vol 21, Iss 6, p 2159 (2020)
International Journal of Molecular Sciences; Volume 21; Issue 6; Pages: 2159

7-Methylguanine (7-MG), a natural compound that inhibits DNA repair enzyme poly(ADP-ribose) polymerase 1 (PARP-1), can be considered as a potential anticancer drug candidate. Here we describe a study of 7-MG inhibition mechanism using molecular dynam

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::102d4cbfca40e6c213d01cb2b4d384af
https://pubmed.ncbi.nlm.nih.gov/32245127

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2,5-Diketopiperazines: A New Class of Poly(ADP-ribose)polymerase Inhibitors

Autor: Alexandra L. Zakharenko, Maria V. Sukhanova, I. V. Gushchina, K. I. Yashina, Vytas K. Švedas, D. K. Nilov, Olga I. Lavrik

Publikováno v: Biochemistry (Moscow). 83:152-158

We show for the first time that natural 2,5-diketopiperazines (cyclic dipeptides) can suppress the activity of the important anticancer target poly(ADP-ribose)polymerase (PARP). Cyclo(L-Ala-L-Ala) and cyclo(L-Ala-D-Ala) can interact with the key resi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3616ba4e471233a26f129f34a9d10089
https://doi.org/10.1134/s0006297918020074

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Structure Modeling of Human TyrosylDNA Phosphodiesterase 1 and Screening for Its Inhibitors

Autor: D. K. Nilov, Olga I. Lavrik, Vytas K. Švedas, Alexandra L. Zakharenko, I. V. Gushchina

Publikováno v: Acta Naturae. 9:59-66

The DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) represents a potential molecular target for anticancer therapy. A human Tdp1 model has been constructed using the methods of quantum and molecular mechanics, taking into account the ionizat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0bd7bf66f7d8bd53901e7ed92361907a
https://doi.org/10.32607/20758251-2017-9-2-59-66

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