TY  - JOUR
A1  - Sarukhanyan, Edita
A1  - Shityakov, Sergey
A1  - Dandekar, Thomas
T1  - In silico designed Axl receptor blocking drug candidates against Zika virus infection
JF  - ACS Omega
N2  - After a large outbreak in Brazil, novel drugs against Zika virus became extremely necessary. Evaluation of virus-based pharmacological strategies concerning essential host factors brought us to the idea that targeting the Axl receptor by blocking its dimerization function could be critical for virus entry. Starting from experimentally validated compounds, such as RU-301, RU-302, warfarin, and R428, we identified a novel compound 2′ (R428 derivative) to be the most potent for this task amongst a number of alternative compounds and leads. The improved affinity of compound 2′ was confirmed by molecular docking as well as molecular dynamics simulation techniques using implicit solvation models. The current study summarizes a new possibility for inhibition of the Axl function as a potential target for future antiviral therapies.
KW  - free energy
KW  - molecular docking
KW  - molecular dynamics
KW  - simulation
KW  - pharmacology
KW  - proteins
KW  - structure-activity relationship
KW  - viruses
KW  - Zika virus
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176739
VL  - 3
IS  - 5
ER  - 
TY  - JOUR
A1  - Isaacs, Darren
A1  - Mikasi, Sello Given
A1  - Obasa, Adetayo Emmanuel
A1  - Ikomey, George Mondinde
A1  - Shityakov, Sergey
A1  - Cloete, Ruben
A1  - Jacobs, Graeme Brendon
T1  - Structural comparison of diverse HIV-1 subtypes using molecular modelling and docking analyses of integrase inhibitors
JF  - Viruses
N2  - The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naïve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance.
KW  - integrase
KW  - naturally occurring polymorphisms
KW  - HIV-1
KW  - molecular modelling
KW  - molecular docking
KW  - diversity
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-211170
SN  - 1999-4915
VL  - 12
IS  - 9
ER  - 
TY  - JOUR
A1  - Sarukhanyan, Edita
A1  - Shityakov, Sergey
A1  - Dandekar, Thomas
T1  - Rational drug design of Axl tyrosine kinase type I inhibitors as promising candidates against cancer
JF  - Frontiers in Chemistry
N2  - The high level of Axl tyrosine kinase expression in various cancer cell lines makes it an attractive target for the development of anti-cancer drugs. In this study, we carried out several sets of in silico screening for the ATP-competitive Axl kinase inhibitors based on different molecular docking protocols. The best drug-like candidates were identified, after parental structure modifications, by their highest affinity to the target protein. We found that our newly designed compound R5, a derivative of the R428 patented analog, is the most promising inhibitor of the Axl kinase according to the three molecular docking algorithms applied in the study. The molecular docking results are in agreement with the molecular dynamics simulations using the MM-PBSA/GBSA implicit solvation models, which confirm the high affinity of R5 toward the protein receptor. Additionally, the selectivity test against other kinases also reveals a high affinity of R5 toward ABL1 and Tyro3 kinases, emphasizing its promising potential for the treatment of malignant tumors.
KW  - Axl tyrosine kinase
KW  - anti-cancer drug-like molecules
KW  - rational drug design
KW  - molecular docking
KW  - molecular dynamics
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-199505
SN  - 2296-2646
VL  - 7
IS  - 920
ER  -