Simian Virus 40 Large T Antigen as a Model to Test the Efficacy of Flouroquinolones against Viral Helicases

Simian virus 40 large T-antigen (SV40 LT-Ag) is a 708 amino acid nuclear phosphoprotein. Among many functions of LT-Ag is its ability to perform as an ATPase-helicase, catalyzing the unwinding of viral genome during replication. The LT-Ag has been employed in the studies of helicase structure and function, and has served as a model helicase for the screening of antiviral drugs that target viral helicase. In this study, using in vitro enzyme assays and in silico computer modeling, we screened a batch of 18 fluoroquinolones to assess their potential as antivirals by virtue of their inhibition of the LT-Ag helicase. We found all fluoroquinolones to be inhibitory to the helicase activity of LT-Ag. In our docking analysis, most of these tested drugs showed similarity in their interactions with LT-Ag. Our study shows the potential of fluoroquinolones as antiviral drugs and of SV40 LT-Ag as a model protein for screening drugs against viral helicases.


Background:
Simian virus 40 (SV40) is a small, non-enveloped DNA virus [1]. The virus' genome comprises two sets of genes: late and early expressed [2]. The late expressed genes encode structural proteins necessary for viral assembly; these include three capsid proteins VP1, VP2, VP3 and a maturation protein agnoprotein [2]. The early expressed genes encode proteins required for viral replication. This set includes the small and large T antigens (ST-Ag and LT-Ag, respectively) [3]. The SV40 LT-Ag is a 708 amino acid nuclear phosphoprotein, with multiple biochemical activities [4]. The LT-Ag is able to transform many cell types; its transforming ability is mainly dependent upon its interaction with cellular factors including retinoblastoma and p53 tumor suppressor proteins [3]. The LT-Ag also acts as a regulator of viral and cellular gene expression, and as an initiator of viral DNA replication [5,6]. The LT-Ag binds to specific sites in the region of SV40 replication origin and promotes the local unwinding of DNA. LT-Ag recruits cellular DNA replication proteins to the site, which include Topoisomerase I, replication protein A, and DNA polymerases, and thus promotes SV40 DNA replication [7].
Among many functions of LT-Ag is also its ability to perform as an ATPase-helicase, catalyzing the unwinding of viral genome during replication, harvesting the energy required for this process by means of ATP hydrolysis [6]. The SV40 LT-Ag is a member of superfamily 3 of helicases, which consists of ring forming helicases [7]. In addition to oncology research, LT-Ag has been employed in the studies of helicase structure and function. The LT-Ag has served as a model helicase also for the screening of antiviral drugs that target viral helicases [8]. In our previous study, LT-Ag was used as a model helicase to develop a non-radioactive helicase assay [9]. For the current study, using in vitro and in silico methods, we screened a batch of 18

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fluoroquinolones to assess their potential as antivirals by virtue of their binding to, and inhibition of, the LT-Ag helicase.

Methodology:
Helicase Assay: Purified SV40 LT-Ag was purchased from CHIMERx, USA. As described previously [9], the helicase substrate was prepared by mixing single strands of complimentary oligonucleotides in 1:1 ratio to a final concentration of 20 µM each, heated to 95°C for 5 min, and then allowed to anneal by gradual cooling to room temperature for 1 hr.

Docking Studies:
To analyze the interactions between LT-Ag and the selected fluoroquinolones, crystal structure of SV40 LT-Ag (PDB ID: 1SVO) was obtained from Protein Data Bank (http://www.rcsb.org), while the SDF files of the fluoroquinolones were obtained from the Pubchem library of the NCBI database (http://www.ncbi.nlm.nih.gov/pccompound). The SDF files were subsequently converted to mol2 format by using OpenBabel GUI [11]. The binding pocket for the drug was predicted using Molegro Virtual Docker (MVD) software. To select the helicase-binding site, coordinates of the binding sphere were designated between Glu473 and Lys445, whereas the radius of search sphere was kept at default setting, i.e., 10Å. To predict protein-ligand interactions, Lead IT or FlexX version 2.0, software was employed [12,13]. The docking was performed using the default parameters of the program, and the Single Interaction Scan algorithm of Lead IT was used for this analysis. This software generates more than 100 docking poses and presents them in ascending order with respect to docking energy. To verify these results, the same analyses were also performed with MVD software.

Docking studies:
The model of SV40 LT-Ag (PDB ID: 1SVO) was docked individually with each of the above-mentioned 18 fluoroquinolones. Each fluoroquinolone was docked deep into the active site of LT-Ag helicase protein molecule. Coordinates of the LT-Ag binding sphere were designated between Glu473 and Lys445. Based on the lowest docking energy, 6 fluoroquinolones, namely, Balofloxacin, Ofloxacin, Pefloxacin, Lomefloxacin, Ciprofloxacin, and Levofloxacin, were selected for detailed analyses of their interactions with LT-Ag (Table 1). Except for Lomefloxacin and Ofloxacin, all six fluoroquinolones showed Hbond interactions with Gly445 and Glu473 in the binding pocket of LT Ag (Table2 and Figure 2). Although it did not form H-bond interactions, amino acid Leu440 was found in the binding pocket of all fluoroquinolones except Lome-and O-floxacin ( Figure 2). Overall, therefore, the interactions made by Lomefloxacin and Ofloxacin were somehow unique compared to other drugs (Table 2 and Figure 2). Based on the free energy values, the affinity of the six drugs for LT-Ag was found to be in the following order: Balofloxacin>Pefloxacin>Lomefloxacin> Ciprofloxacin > Levofloxacin >Ofloxacin ( Table 1). The same order was recapitulated when the docking energy of these fluoroquinolones were calculated using a different software, namely, Molegro (Table 1). Overall, Molegro recapitulated the interactions between fluoroquinolones and SV40 LT-Ag (data not shown).

Discussion:
In this study we have used SV40 LT-Ag as a model viral helicase and have explored the inhibitory interactions of fluoroquinoloneson with this enzyme using in vitro as well as in silico approaches. We tested the activity of a panel of 18 fluorquinolones using a helicase assay and found all of them to inhibit the helicase activity of LT-Ag. Docking of these fluoroquinolones on LT-Ag was also performed using in silico methods. Based on the free energy values, 6 fluoroquinolones were found to interact most strongly with LT-Ag, with their binding affinities in the following order: Balofloxacin>Pefloxacin>Lomefloxacin>Ciprofloxacin>Levofloxa cin >Ofloxacin. Docking analysis identified certain amino acids in the LT-Ag active site, namely, Gly445, Glu473, and Leu440 that were found to interact frequently with most of the six selected fluoroquinolones. For this study, we employed the nonradioactive assay that we have previously published [10]. In this assay, 18 different fluoroquinolones were tested on LT Ag helicase activity. All of the tested drugs showed inhibition of helicase activity to some degree. Most fluoroquinolones showed inhibition of 40%-80% at 10uM and 30%-60% at 1uM. In our
The current results are therefore consistent with previous reports.

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understanding of the differential interaction of fluororoquinolones on different helicases may be obtained by analyzing crystal structures of helicase-fluoroquinolone complexes and/or by studying the effect of amino acid mutations in the active site of LT-Ag. For the current study, we adopted an in silico approach to further dissect the interactions of fluoroquinolones at the LT-Ag active site.
Computer docking models of fluoroquinolone-LT-Ag helicase also revealed certain key functional groups of fluoroquinolone that were involved in their mutual interaction with LT-Ag helicase. The docked models of fluoroquinolones and LT-Ag showed that the piperazinyl moiety at position 7, carboxylic acid at position 3 and oxoquinoline at position 4 in the fluoroquinolone molecule were mostly involved in interaction with the amino acid residues of LT-Ag. The docking output reflected binding efficiency of LT-Ag and fluoroquinolones. The binding affinity of Balofloxacin was the highest followed by affinities for Pefloxacin, Lomefloxacin, Ciprofloxacin, Levofloxacin, and Ofloxacin (-16.4, -16.1, -15.6, -15.0, -14.0, and -13.6, kJ/mol, respectively), as predicted by FlexX ( Table 1). The same trend was recapitulated when the docking of these drugs was performed using Molegro. All of these fluoroquinolones also showed 60-70% inhibition of helicase activity at 10µM concentration in in vitro helicase assay (Figure 1). The molecular interaction between Ofloxacin and SV40 LT-Ag was found to be weakest as judged by docking energy scores (-13.6), which was in agreement with in vitro assay results, where at 10µM concentration it showed less than 60% inhibition of helicase activity (Figure 1). It may be concluded, therefore, that the energy scores roughly correlated with the performance of fluoroquinolones in the invitro assays. On a deeper level, discrepancies in a drug's in situ and in vitro behavior may also be attributed to the behavior of the drug in solution, and the effects of environmental factors, such as pH and temperature. Interestingly, Ofloxacin and Lomefloxacin showed interactions that were unique from all the other fluoroquinolones we studied. Since, structurally, Ofloxacin and Lomefloxacin are not remarkably different from the rest of the drugs; it is possible that the in situ spatial orientation of these two fluoroquinolones differs from the other drugs we studied. This may be further explored by deeper analysis of docked fluroquinolone-LT-Ag complexes. It would be interesting to design in silico derivatives of fluoroquinolones, combining features of Ofloxacin and Lomefloxacin with other fluoroquinolones, and study their docked complexes with LT-Ag and other helicases. This exercise may provide fluroroquinolone derivatives that inhibit the helicase activity more strongly than the existing drugs.