In silico and in vitro methods to identify ebola virus VP35-dsRNA inhibitors

Abstract

Ebola virus continues to be problematic as sporadic outbreaks in Africa continue to arise, and as terrorist organizations have considered the virus for bioterrorism use. Several proteins within the virus have been targeted for antiviral chemotherapy, including VP35, a dsRNA binding protein that promotes viral replication, protects dsRNA from degradation, and prevents detection of the viral genome by immune complexes. To augment the scope of our antiviral research, we have now employed molecular modeling techniques to enrich the population of compounds for further testing in vitro. In the initial docking of a static VP35 structure with an 80,000 compound library, 40 compounds were selected, of which four compounds inhibited VP35 with IC50 < 200uM, with the best compounds having an IC50 of 20 uM. By superimposing 26 VP35 structures, we determined four aspartic acid residues were highly flexible and the docking was repeated under flexible parameters. Of 14 compounds chosen for testing, five compounds inhibited VP35 with IC50 < 200uM and one compound with an IC50 of 4 uM. These studies demonstrate the value of docking in silico for enriching compounds for testing in vitro, and specifically using multiple structures as a guide for detecting flexibility and provide a foundation for further development of small molecule inhibitors directed towards VP35.

Insights into Ebola Virus VP35 and VP24 Interferon Inhibitory Functions and their Initial Exploitation as Drug Targets

“…Although the increasing and constant effort in the identification of VP35 and VP24 inhibitors and despite recent progresses have been made in developing novel techniques to test their functions, nowadays no approved drugs are available against these promising pharmacological targets. These studies involved in vitro, in vivo and in silico approaches aimed to identify potential inhibitors among small molecules and FDA-approved drugs, plant extracts or compounds, oligomers, peptides and immune therapies [16,18,19,63,[102][103][104][105][106][107][108][109][110][111][112][113] Figure 5. VP35 and VP24 inhibitors.…”

“…The search space for docking specifically included the CBP of VP35 IID and the residues known to be involved in the dsRNA binding: R305, K309, R312, K319, R322 and K339 of which residues R305, K339, K309 and R322 were designated as flexible. Among compounds with the highest predicted affinity, ZINC05328460 ( Figure 5) showed the greatest inhibition of VP35-dsRNA binding (IC50: 4 µM) [105].…”

Inappropriate modeling of chronic and complex disorders: How to reconsider the approach in the context of predictive, preventive and personalized medicine, and translational medicine

“…Living systems refer to systems based on animal or human components such as cell, tissue, and organ cultures and systems based on organisms including microorganisms, lower vertebrates, and invertebrates. Non-living systems such as biochemical and physiochemical systems, mathematical and computer models (in silico analysis) [110], and epidemiological data on human can also be applied when there is adequate information accessible [83,107,111,112]. A number of alternative methods are listed in Table 1.…”

A cryptic pocket in Ebola VP35 allosterically controls RNA binding

“…As a result, attempts to rationally design small molecules that bind these interfaces have not yielded sufficiently strong leads to warrant clinical development. 33,34 The discovery of cryptic pockets in VP35 could provide new opportunities for drugging this essential viral component. Figure 1.…”