1. 1
2010
Discovery & Development of
a First in Class Anti-Ebola
Drug- EBONAVIR®
Summary:
Ebola hemorrhagic fever (Ebola HF) caused by the Ebola virus
is a severe, often-fatal viral hemorrhagic disease in humans and
nonhuman primates with a fatality rate of 50-83%. The present
document details the discovery and development of a novel
small molecule organo-pharmaceutical that acts as a potent
inhibitor of VP35 - a critical protein involved in EBOV
pathogenesis through early preclinical studies as well as
clinical studies. It provides an insight into the research,
documentation and regulatory requirements pertaining to the
commercial launch of the above mentioned small molecule
drug.
GAYATHRI VIJAYAKUMAR
MS Biotechnology, NYU-POLY
5/1/2010

2. 2
CONTENTS
1) Introduction 5
a) Ebola Virus 5
b) Transmission 5
c) Symptoms 5
d) Diagnosis 6
e) Treatment 6
f) History 6
2) Current therapeutic advances for Ebola Hemorrhagic Fever 6
3) Promising targets for development of therapeutics 7
4) Target for drug development 8
a) Reason for selection of VP35 as a therapeutic target 8
b) Impairment of innate immunity 10
5) Medical hypothesis for developing an anti-Ebola therapeutic 12
6) Conclusion regarding medical hypothesis 14
7) Assays for HTS screening of potential anti-Ebola therapeutic 15
a) Luciferase Budding Assay 15
b) Immunocapture Assay 16
c) Cell based assay using recombinant GFP-ZEBOV 16
8) Luciferase Reporter based gene assay selected for HTS screening 18
a) Illustration of principle 21
9) Lead Compound 22
a) Selected Lead Compound candidate 24
10) Lead Optimization 25
a) Lead Optimization results 26
11) In vitro safety pharmacology profiling 28
a) In vitro SPP Profile results 33
12) Patent Application 35
13) Selection of appropriate animal model for efficacy evaluation of the selected NCE 36
a) Mouse model used for preclinical studies 38
b) Non-human primate model used for preclinical studies 40

3. 3
14) Biomarkers 42
a) Disease Biomarkers 43
b) Surrogate Biomarker 45
c) Toxicity Biomarker 45
d) Target Biomarker 46
e) Mechanism Biomarker 46
f) Efficacy Biomarker 47
g) Translational Biomarker 47
h) Stratification Biomarker 47
15) Efficacy studies for Minimum Effective Dose 48
a) Minimum Effective Dose 49
16) Principal studies in animal models with NCT1087 49
a) Animal models in safety studies 50
b) Route of Administration of NCT1087 51
c) Safety Pharmacology Studies 51
d) Acute Toxicity Study 53
e) Repeated Dose Toxicity Study 53
f) Genetoxicity Study 55
g) Carcinogenicity Study 57
h) Reproduction Toxicity Study 57
i) Immunotoxicity Study 58
j) Phototoxicty Study 59
17) Maximum Tolerated Dose 60
a) Toxicity studies for determining the MTD 60
18) Repeated dose toxicity studies for 2 months 62
19) Estimation of the first human dose 64
20) IND Application 65
21) Phase I Clinical Trials 67
22) Phase II Clinical Trials 71
23) Phase III Clinical Trials 77
24) Conclusion 83
25) Route of Delivery, Administration Regimen & Dose Concentration 83
26) NDA Application 84
27) Life Cycle Management of NCT1087 or Ebonavir® 85
28) The Drug Development process 86

4. 4
29) Preclinical & Requirements for IND, NDA &Clinical studies 88
30) CMC Requirements for IND, NDA & Clinical studies 89
31) Possible Emergence of Resistance to Ebonavir® 90
32) References 91

5. 5
EBOLA HEMORRHAGIC FEVER
Ebola hemorrhagic fever (Ebola HF) is a severe, often-fatal viral hemorrhagic
Figure 1. [3]
disease in humans and nonhuman primates (monkeys, gorillas, and chimpanzees)
that has appeared sporadically since its initial recognition in the Democratic Republic
of Congo in 1976 [1]. It is caused by the Ebola Virus which interferes with the
interior endothelial cell lining of blood vessels and coagulation which leads to
hypovolemic shock [2]. Destruction of endothelial surfaces is associated with
disseminated intravascular coagulation, and this may contribute to the
hemorrhagic manifestations [5]. Fatality rate differs from 50-83% [2]. [3]
EBOLA VIRUS (shown in image [6])
Figure 2. [6]
The Ebola virus belongs to the Filoviridae family (filovirus) and is
comprised of five distinct species: Zaire, Sudan, Côte d’Ivoire, Bundibugyo and
Reston. [4] The Zaire virus (ZEBOV) is the most lethal with an average case
fatality rate of 83% [2]. Ebola virus has a non-segmented, negative-stranded, RNA
genome containing 7 structural and regulatory genes [5]. The exact origin,
locations, and natural habitat (known as the "natural reservoir") of Ebola virus
remain unknown. Researchers believe that the virus is zoonotic (animal-borne) [4].
Electron microscopic image of an Ebola infected cell in [9] (Figure 3).
TRANSMISSION
1) Direct contact with the blood and/or secretions of an infected person/ animal
[1].
2) Contact with objects, such as needles, that have been contaminated with
infected secretions [1].
3) Nosocomial transmission refers to the spread of a disease within a health-
care setting, due to incorrect infection control precautions and adequate
barrier nursing procedures [1, 4]
Figure 3: [9]
SYMPTOMS
The incubation period for Ebola HF ranges from 2 to 21 days. The onset of illness is abrupt and
is characterized by fever, headache, joint and muscle aches, sore throat, and weakness, followed by diarrhea,
vomiting, and stomach pain. A rash, red eyes, hiccups and internal and external bleeding may be seen [1].

6. 6
DIAGNOSIS
Diagnosis is usually done with inactivated blood or saliva specimens to detect the viral antigen/antibody or
genetic material [4]. They can also be isolated in cell cultures. Diagnostic laboratory tests such as ELISA, RT-PCR,
IgM ELISA, Immunohistochemistry testing, Coagulation studies; Complete Blood Count, etc are usually performed
[1,7].
TREATMENT
There is no standard treatment for Ebola hemorrhagic
fever. Treatment is primarily supportive and includes minimizing
invasive procedures, balancing electrolytes, and, since patients
are frequently dehydrated, replacing lost coagulation factors to
help stop bleeding, maintaining oxygen and blood levels, and
treating any complicating infections. Convalescent plasma,
administration of an inhibitor of coagulation (rNAPc2),
Morpholino antisense drugs have shown some promise in
treatment for Ebola HF [2].
HISTORY
History of Ebola virus outbreaks have been shown in the
table to the side (Figure 4). Confirmed cases of Ebola HF have
been reported in the Democratic Republic of the Congo, Gabon,
Sudan, the Ivory Coast, Uganda, and the Republic of the
Congo. [1] Because of its high morbidity, it is a potential agent
for bioterrorism and since no approved vaccine or drugs are
available it is classified as a biosafety level 4 agents as well as
Category A bioterrorism agent by the CDC [2]. The last
reported outbreak was in December 2008 in the Western Kasai
province of the Democratic Republic of Congo [2].
Figure 4: From [8]
CURRENT THERAPEUTIC ADVANCES FOR EBOLA HEMORRHAGIC FEVER
To date, beyond supportive care, no effective treatments, therapies, or vaccines are approved to treat or
prevent Ebola virus infections because natural immunity to this infection is difficult to find, plus there are no immune
correlates in humans [10]. However, several drugs are under development as summarized:

7. 7
• USAMRID investigated a drug called recombinant nematode anticoagulant protein C2 (rNAPC2) which blocks
the harmful effects of tissue factors and targets the disease process. It showed reasonable success in infected
rhesus monkeys [11].
• AVI BioPharma’s proprietary NEUGENE drug targets a key Ebola gene providing complete protection in mice
when administered either before or after an otherwise lethal infection with Ebola virus. NEUGENE antisense
compounds are synthetic polymers designed to match up perfectly with a specific gene or viral sequence,
blocking the function of the target gene or virus [12].
• Phosphorodiamidate morpholino oligomers (PMO) are a class of uncharged single-stranded DNA analogs
modified such that each subunit includes a phosphorodiamidate linkage and morpholinering. Data suggest that
antisense PMO and P-PMO have the potential to control EBOV infection and are promising therapeutic
candidates [13]. A combination of EBOV-specific PMOs targeting sequences of viral mRNAs for the viral
proteins (VPs) VP24, VP35 has been used as both pre- and post- exposure therapeutic regimens in non-human
primates [14].
• NanoViricides, Inc. has come out with broad-spectrum nanoviricides(TM) drug candidates that have been found
to be highly effective in cell culture studies by USAMRID. These antivirals use biomimetic technology (i.e. they
mimic the host cell features) [15].
• 3-Deazaneplanocin A, an analog of adenosine, is a potent inhibitor of Ebola virus replication. A single dose early
in infection prevents progression of the disease in EBOV infected mice. Protective effect of the drug results from
massively increased production of interferon-α [17].
• Cyanovirin-N (CV-N) which is an HIV inactivating protein has been found to have both in vitro and in vivo
antiviral activity against the Zaire strain of the Ebola Virus by inhibiting the development of viral cytopathic
effects (CPEs). It has been found to delay fatality in EBOV infected mice. It binds with considerable affinity to the
Ebola envelope glycoprotein GP1,2 . [19].
• EBOV infected immunocompetent mice treated with the adenosine analogue carbocyclic 3-deazaadenosine
protects it against fatality by blocking the cellular enzyme S-adenosyl-L -homocysteine hydrolase (SAH) [20].
• A vaccine based on recombinant vesicular stomatitis virus expressing the ZEBOV glycoprotein has been found
to confer immunity against aerosol challenge in cynomolgus macaques which is likely to be the port of entry in a
bioterrorist attack [21].
• Intranasal vaccine based on replication-competent human parainfluenza virus type 3 (HPIV3) expressing EBOV
glycoprotein GP (HPIV3/EboGP) and showed that it is immunogenic and protective against a high dose
parenteral EBOV challenge [22].
PROMISING TARGETS FOR DEVELOPMENT OF THERAPEUTICS
An eight amino acid sequence (TELRTFSI) present in the carboxy terminal end (aa 577–584) of membrane-
anchored GP, the major structural protein of Ebola virus, was identified as an H-2k-specific murine cytotoxic T cell
epitope. Immunity can be stimulated by injecting irradiated Ebola virus encapsulated in liposomes containing lipid A
[16].

8. 8
Figure 5. Ebola Virus Potential targets
• RNA is blocked by inhibiting the cellular enzyme SAH, indirectly
[10].
resulting in reduced methylation of the 5′ cap of viral mRNA [17].
• NSecretary glycoproteins can be targeted by neutralizing
monoclonal antibodies [18].
• VP24, VP30 and VP40 can induce protective immune
responses [23].
• SCripps Research Institute found that VP35 is critical in
allowing uncontrolled replication by fooling the human immune
system [24].
In my opinion there definitely exists a medical need as
1) there are no approved therapies yet in the market, 2) it has a fatality of 50-80%, 3) it is a potential bioterrorism
agent, but it is definitely not an impossible task which is clearly observable from all the latest developments in the
field and all the possible targets available for developing a potential therapy.
TARGET FOR DRUG DEVELOPEMENT
The target that I have selected for development of a therapy against EBOV infection is the virion protein VP35.
Reason for selection of VP35 as a therapeutic target
The 18.9-kb RNA genome of EBOV is non-infectious and encodes
seven structural proteins and one non-structural protein in the following order
within the genome: 3′ non-coding region (leader), nucleoprotein (NP), virion
protein 35 (VP35), VP40, glycoprotein (sGP and GP), VP30, VP24, RNA-
dependant RNA-polymerase (L) protein and 5′ non-coding region (trailer)
[27]. Mature EBOV particles form long filamentous rods with a uniform
diameter of 80 nm and a mean length of 1250nm. Virus particles possess a
central core, known as the ribonucleoprotein (RNP) complex that consists of
NP, VP35, VP30, L and the viral RNA. This RNP complex is surrounded by a
lipid envelope, with which the remaining proteins GP1,2, VP40 and VP24 are
associated; these three proteins function as surface glycoprotein, major
matrix protein and minor matrix protein, respectively as shown in the figure
on the side. (Figure 6; [27]) Figure 6. [27]
Three pathogenic mechanisms that underlie EBOV infection are vascular instability, coagulopathy and
immunosupression (Figure 7; [27]. Besides the induction of cytopathic cytotoxicity in epithelial and endothelial
cells (which perhaps explains the hemorrhagic manifestations characteristic of filovirus infection), destruction
of the immune system is another significant feature of EBOV infection. The EBOV infects the mononuclear
phagocyte and fibroblastic reticular systems associated with lymph nodes which maximizes immune

9. 9
responses by activation of appropriate cytokine production and antigen trafficking. This results in inadequate
development of immunity, thus playing an important role in pathogenesis [25].
Recent data shows that the EBOV virus VP35 protein, which plays an essential role in viral RNA synthesis,
acts as a type 1 IFN antagonist in much the same way as the NS1 protein, another IFN antagonist, enhances the
replicative ability of influenza virus, indicating that the presence of such a protein could be required for full
expression of virulence [25]. Nucleoproteins VP-35 and -30 and RNA polymerase are required for RNA transcription
and replication [25]. Another study found that the formation of nucleocapsid structure doesn’t occur in the absence
of VP35, VP24 or NP [26].
Figure 7: Overview of the mechanisms that are involved in EBOV pathogenesis. taken from [27].

10. 10
Impairment of innate immunity
EBOV infection attacks the innate and adaptive immunity by
• Inflammatory responses that are accompanied by substantial cytokine production [27].
• DCs, which have a crucial role in both innate and adaptive immunity, fail to fulfill their function after
infection by not producing proinflammatory cytokines or express co-stimulatory molecules such as CD80
or CD86, are impaired in their ability to support T-cell proliferation and undergo anomalous maturation
[27].
• Depletion of NK cells and lymphocytes [27].
• EBOV selectively suppresses responses to IFN-α and IFN-γ and the production of IFN-α in response to
double-stranded RNA [27].
• Blockade of IFN signaling has an important role in the pathogenesis of EBOV infection in vivo [27].
VP35 blocks phosphorylation of the IFN-regulatory factor 3 (IRF3), which acts as a transcription factor for
IFN production, whereas VP24 seems to block IFN signaling indicating that the block of IFN signaling might be
due to inhibition of p38 phosphorylation, which is central in the mitogen-activated-protein-kinase (MAPK) p38
IFN-signaling pathway [27].
During virus infection, RNAi against the virus is activated
by the production of virus-specific double-stranded RNAs (RNA
interference (RNAi) mechanism). Similar to RNAi, the IFN
pathway is triggered by cytoplasmic viral dsRNAs and acts as a
sensitive and potent antiviral response that is involved in innate
and subsequent adaptive immunity. To overcome this antiviral
RNAi response, viruses encode RNA silencing suppressors
(RSSs) and these include the influenza A virus NS1 (NS1),
vaccinia virus E3L (E3L), hepatitis C virus Core, primate foamy
virus type 1 (PFV-1) Tas, and the HIV-1 Tat proteins, as well as
the adenovirus virus-associated RNAs I and II (VAI and VAII).
Figure 8. RNA Interference Mechanism [28]
Strikingly, all RSS proteins from mammalian viruses possess IFN
or protein kinase R (PKR) antagonistic properties, suggesting
that RNAi and other innate antiviral responses are interrelated. A
study showed that Ebola virus (EBOV) VP35 protein is a potent
RNAi suppressor that is functionally equivalent to the HIV-1 Tat RSS function [28].

11. 11
Although the importance of antiviral RNAi responses in plants, nematodes, and insects is firmly
established, it is still under debate whether RNAi has a similar function in mammalian cells. But all the same
the above study demonstrates the importance of VP35 in helping EBOV in avoiding detection by the immune
system [28].
Another study showed that the Ebola virus VP35 protein is a virus-encoded inhibitor of the type I IFN
response. VP35 subsequently was shown to block double-stranded RNA- and virus-mediated induction of an
IFN-stimulated response and to block double-stranded RNA- and virus-mediated induction of the IFN-β
promoter. Type I IFN is synthesized in response to viral infection; double-stranded RNA (dsRNA) or viral
infection activates latent transcription factors, including IRF-3 and NF-κB, resulting in the transcriptional up-
regulation of type I IFN, IFN-α, and IFN-β, genes. Secreted type I IFNs signal through a common receptor,
activating the JAK/STAT signaling pathway. This signaling stimulates transcription of IFN-sensitive genes,
including a number that encode antiviral proteins, and leads to the induction of an antiviral state. Among the
antiviral proteins induced in response to type I IFN are dsRNA-dependent protein kinase R (PKR), 2′,5′-
oligoadenylate synthetase (OAS), and the Mx proteins [29].
This study validates that Ebola virus VP35 is therefore likely to inhibit induction of type I IFN in Ebola
virus-infected cells and may be an important determinant of Ebola virus virulence in vivo [29].
Figure 9.This image shows the crystal structure of the Ebola virus protein VP35 bound to a molecule of double-
stranded helical RNA (green). Two VP35 molecules come together to mask the end of the double-stranded RNA
helix from detection by the immune system. The interface between the two VP35s (white) may provide new targets
for drugs to counteract the virus. [30]

12. 12
Medical Hypothesis for developing an anti-EBOV Therapeutic
The Ebola VP35 protein is multifunctional, acting as a component of the viral RNA polymerase complex,
a viral assembly factor, and an inhibitor of host interferon (IFN) production [31]. All the studies above have
established the fact the VP35 is absolutely essential for Ebola virus pathogenesis as well virulence.
Therefore I conclude that it makes an excellent target for development of a therapeutic. From whatever
scientific publications I have read so far, I think that there are two ways you can tackle this problem.
1. Using antisense Phosphorodiamidate morpholino oligomers
They are a class of uncharged single-stranded DNA analogs modified such that each subunit
includes a phosphorodiamidate linkage and morpholine ring [13]. Data suggests that antisense
PMO and P-PMO (PMO conjugated to arginine-rich cell-penetrating peptide) have the potential to
control EBOV infection by binding to the translation start site region of EBOV VP35 positive-sense
RNA and generating sequence-specific and time- and dose-dependent inhibition of EBOV
amplification in cell culture [13]. AVI BioPharma’s proprietary NEUGENE drug uses a combination
of EBOV-specific PMOs targeting sequences of viral mRNAs for the viral proteins (VPs) VP24,
VP35, and RNA polymerase L and found it to have reasonably good success in EBOV-infected
rodents and primates. It is currently under clinical trials [14].
2. Targeting C-terminal of VP35 IID
Mutation of select basic residues within the C-terminal half of VP35 inhibits its dsRNA-binding
activity, impairs VP35-mediated IFN antagonism, and attenuates EBOV growth in vitro and in vivo
[31]. A functional VP35 is required for efficient viral replication and pathogenesis; knockdown of
VP35 leads to reduced viral amplification and reduced lethality in infected mice [31]. VP35
contains an N-terminal coiled-coil domain required for its oligomerization (required for viral
replication) and a C-terminal dsRNA-binding region (blocks signaling that triggers IFN process)
[31]. Data suggest that the dsRNA binding activity mediated by the C terminus of VP35 is critical
for viral suppression of innate immunity and for virulence. There are 2 basic patches that are
highly conserved among members of the Filoviridae family (identical among EBOV isolates).
Biochemical and NMR-based structural analyses show that one patch contains residues that are
required for dsRNA binding and IFN inhibition, whereas the functional significance of the other
basic patch remains unknown [31]. Therefore a compound that would target the conserved region
in the C-terminal of VP35 IID which are critical for dsRNA binding may result in impaired IFN
suppression and yield attenuated viruses in vivo because of reduced dsRNA binding ([31]; see
Figures 10-12 below).

13. 13
Figure 10. Crystal structure of VP35 C-terminal IFN-inhibitory domain (IID) reveals a fold that binds dsRNA. (A)
Domain organization of VP35. (B) Ribbon representation of VP35 IID. Secondary structural elements that form the
α-helical subdomain (orange) and the β-sheet subdomain (yellow). (C) Topology and delimiting sequence markers
of VP35 IID [31].
Figure 11. Polymerase cofactor VP35, Key word 3FKE [32]. Figure 12. Structures of the
] Ebola VP35 IID dsRNA
binding domain [31].

14. 14
CONCLUSION
A molecule or compound that inhibits VP35 of the Ebola virus will inhibit binding of the virus-specific dsRNA
produced by the host cell as part of RNA interference (RNAi) mechanism thus activating both double-stranded
RNA- and virus-mediated induction of an IFN-stimulated response as well as double-stranded RNA- and virus-
mediated induction of the IFN-β promoter [28][29]. This activated latent transcription factors, including IRF-3 and
NF-κB, resulting in the transcriptional up-regulation of type I IFN, IFN-α, and IFN-β, genes. Secreted type I IFNs
signal through a common receptor, activating the JAK/STAT signaling pathway. This signaling stimulates
transcription of IFN-sensitive genes, including a number that encode antiviral proteins, and leads to the induction of
an antiviral state [29]. This leads to up regulation of the innate immune system.
Virus-specific dsRNAs on the other hand are processed into small interfering RNAs (siRNAs; a 21-
nucleotide dsRNA duplex) by the RNAse III–like endonuclease-denoted Dicer. Subsequently, one strand of the
siRNA duplex, the guide-strand, is incorporated into the RNA-induced silencing complex (RISC) to target viral
mRNAs bearing complementary sequences for destruction. [28]
Thus I conclude that a compound that inhibits VP35
leads to activation and up regulation of the innate and
adaptive immune system. In addition inhibition of VP35
exposes viral mRNAs to host cell antiviral response. This
leads to reduction in the viral load, and thus will stop
progression of the infection.
Why is my target better?
I think that this target is better than the others
• As scientific evidence doesn’t prove that inhibition
of other viral targets will elicit the same degree of
recovery as VP35 inhibition.
• VP35 is very integral to EBOV replication and
pathogenesis.
Figure 13: Model for VP35-mediated
• C-terminal of VP35 IID is conserved among members
IFN inhibition and immune
of the Filoviridae family (identical among EBOV isolates). suppression [31].

15. 15
ASSAY FOR HTS SCREENING OF POTENTIAL ANTI-EBOLA THERAPEUTICS
There are a few assays that are in use for Ebola research. It is listed as follows along with their principle and a brief
description of their methodology.
LUCIFERASE BUDDING ASSAY
It is a functional budding assay that has been developed based on the ability of VP40 matrix protein of EBOV in
bringing about the budding of virus-like particles (VLP) from mammalian cells. This well-defined assay has been
modified for potential use in a high-throughput format in which the detection and quantification of firefly luciferase
protein in VLPs represents a direct measure of VP40 budding efficiency. Luciferase was found to be incorporated
into budding VP40 VLPs. In contrast, when luciferase is co-expressed with a budding deficient mutant of VP40,
luciferase levels in the VLP fraction decrease significantly. Although VP40 does not require the presence of
additional viral proteins to achieve VLP egress, the contribution of glycoprotein (GP), nucleoprotein (NP), VP35 and
VP24 to budding has been studied.
BRIEF DESCRIPTION OF THE METHODOLOGY
Human 293 T cells are grown in DMEM supplemented with
10% FCS and 1% penicillin-streptomycin at 5% CO2at 37OC.
pCAGGS-luciferase vectors are constructed by insertion of
luciferase into the SacI and NsiI sites of the pCAGGS vector.
Subsequently, VP40 is joined to the C-terminal end of
luciferase by insertion into the NsiI and XhoI sites of pCAGGS-
luciferase. One hundred millimeter plates of 293T cells are
transfected with 10µg of each plasmid DNA using
Lipofectamine in OptiMem. Cells are metabolically labeled 24h
post-transfection with Met-Cys. Six hours later, media was
harvested, clarified, and layered over a 20% sucrose cushion
in STE buffer, then centrifuged. The pellet was resuspended in Figure 14. Luciferase activity in VLPs correlates
STE buffer and lysed with radioimmunoprecipitation assay with expression and budding efficiency of VP40.
Human 293T cells were transfected with pCAGGS +
(RIPA) buffer. Cells were washed twice with PBS and then luciferase, VP40 + luciferase, VP40 + GP +
lysed in RIPA buffer. Both cells and VLP lysates were luciferase, or VP40d-PT/PY + luciferase. VLPs were
isolated and then combined with luciferase reagent.
immunoprecipitated with the appropriate antibodies and Relative light units (RLU) were measured using a
analyzed by SDS polyacrylamide gel electrophoresis (PAGE) luminometer. The RLU value of luciferase +
pCAGGS was normalized to one [33].
[33].
Subsequently Protease Protection assay and VLP Luciferase Assay was performed [33],

16. 16
IMMUNOCAPTURE ASSAY
It is basically a rapid ELISA assay that detects both Ebola virus and EBOV-like particles (VLPs) directly from cell-
culture supernatants with the VP40 matrix protein serving as antigen. This assay can be used in surrogate models
in non-biocontainment environment, facilitating both basic research on the mechanism of EBOV assembly and
budding as well as drug-discovery research. Such an assay could also replace or be complementary to the
conventional viral plaque assays for virus detection, which require more than a week to accomplish [34].
BRIEF DESCRIPTION OF METHODOLOGY
cDNA for EBOV Zaire NP, VP30, VP35, and VP24 was cloned
into pWRG7077 vector. Polyclonal anti-VP40 antibody was
generated by immunizing rabbits with a peptide corresponding to
the N-terminal 15 amino acids of VP40 protein. Sera from
convalescent EBOV-infected guinea pigs were used as the
polyclonal anti-EBOV antibody. Bacterial expression of EBOV
VP40 was done by using a pET16b-VP40 clone to introduce a
His6-fusion at the N-terminus in E.coli. Subsequently purification
and extraction of EBOV VP40 was done from the cell lysate.
Fractions were analyzed by SDS-PAGE and appropriate
fractions were pooled [34].
HB 96-well plates were coated with AE11 monoclonal mouse
anti-VP40 antibodies. The plates were washed with PBST.
PBST containing 5% milk was added to block non-specific
binding sites. After binding, plates were washed with PBST.
Cellular extracts or culture supernatants were loaded with 1% Figure 15. Establishing an EBOV VP40 ELISA. (A)
Coomassie staining of purified VP40 protein (lane 1).
milk PBST. The samples were removed and the wells washed Immunoblotting of VP40 protein gel using anti-VP40
three times for 5 min. Rabbit polyclonal anti-VP40 antibodies antibodies showing the monomeric and oligomeric
forms of VP40 (lane 2). (B) Standard curve for VP40
were added in PBST/5% milk and incubated for 1 h. The plate
ELISA generated using purified VP40 protein. (C)
was washed again and anti-rabbit HRP-conjugated antibodies Standard curve for VP40 ELISA using inactivated
were added in PBST for 30 min. The plate was washed with EBOV lysed in 1.5% Triton X100. Capture antibodies
were monoclonal mouse anti-VP40 and detection
PBST and PBS. HRP substrate was added to each well and antibodies rabbit anti-VP40 polyclonal antisera [2].
absorbance at 650 nm was read [34].
CELL-BASED ASSAY USING RECOMBINANT GFP-ZEBOV
In this assay the GFP acts as a receptor for virus replication. As such this assay can be used to screen compounds
that inhibit replication of the virus [35]

17. 17
BRIEF DESCRIPTION OF METHODOLOGY
Confluent Vero E6 cells (96-well plate format) were pretreated
with compound (drug) diluted in cell-culture medium for 18h.
Cells were then infected with GFP-ZEBOV. Compound was
reapplied to cells after infection by adding media containing the
same pretreatment concentration. Cultures were incubated for
48h before fixation. After nuclear staining (Hoechst dye), viral
infection was determined using a high content imaging system,
Discovery 1, which compiles GFP fluorescence data from
approximately 25,000 cells per well. This procedure identifies
the total number of adherent cells, and fraction of infected
cells, thus providing an immediate assessment of efficacy and Figure. 16: FGI-106 blocks Ebola virus infection. (A)
Vero E6 cells were infected with Zaire-Ebola virus
toxicity. Validation of the results was done by means of Virus
(ZEBOV) for 72 h in the presence of 0–4 µM FGI-106.
Yield Reduction Assay. [35] Antiviral efficacy was evaluated using plaque assays
of infectious Ebola particles to assess the number of
Another paper which utilizes the same principle engineered an plaque forming units per unit volume (pfu/mL). (B)
The number of viable Vero E6 cells was assessed
EboZ-eGFP by inserting eGFP open reading frame preceded
following 72 h incubation in the presence of the
by a 90-nucleotide fragment containing an authentic indicated concentrations of FGI-106. (Drug) [35]
transcription stop sequence, to direct the termination of the NP
mRNA, and a transcription start sequence to direct the
initiation of the eGFP message into the cloned BsiW1
restriction site present in the NP 3′ UTR. The “wild-type like”
virus was termed EboZ-BsiW1. As a proof of principle for using
the EboZ-eGFP virus to rapidly screen antiviral compounds,
consensus interferon alpha (conIFN-α), a compound with
known EboV antiviral properties, was used at multiple
concentrations to treat Vero E6 cells infected with either EboZ-
eGFP virus or a control Zaire ebolavirus. The infected cells
were monitored for evidence of virus replication by either
fluorescence microscopy (for EboZ-eGFP virus) or a previously
published CPE-based assay [37].
Figure 17: (A) Time course of Vero E6 cells infected with EboZ-
eGFP, EboZ-BsiW1, or EboZ-wt. Vero E6 cells were infected at a
MOI of two and virus (B) Fluorescent microscopy of human PBMCs
either mock-infected or infected with EboZ-eGFP and analyzed at the
indicated times post-infection. (C) Electron micrograph of a human
macrophage infected with EboZ-eGFP virus [37].

18. 18
PLAQUE ASSAY FOR EBOLA VIR
PLAQUE ASSAY
Confluent Vero cells are infected with an EBOV strain. After
absorption of the viral innoculum for 1h, 30 ml of EBM containing
5% FBS, antibiotics and HEPES buffer are incubated in flasks
for 10 days. Harvested medium is centrifuged and the
supernatant fluid is made into dilutions using L-15 medium and
inoculated into monolayers of cell lines being tested. After
various incubation periods, cell monolayers are stained using an
agarose overlay containing neutral red. Plates are then
examined for plaques 24 and 48 hours after adding the stain
overlay. The viral origin of the plaques is verified by inoculating
one of the plaques mixed with L-15 medium into suckling mice.
After death of the mice, the livers are removed, processed for
virus isolation, and examined for viral antigens with the IFA
procedure. Liver tissue collected from mice which had died post-
inoculation will show EV-specific fluorescence by IFA and from
this the PFUs can be counted [36].
Figure 18: From [36].
THE ASSAY THAT IS SELECTED FOR HTS SCREENING-A LUCIFERASE
REPORTER BASED GENE ASSAY
PRINCIPLE:
The Ebola VP35 protein is multifunctional, acting as a
component of the viral RNA polymerase complex, a viral
assembly factor, and an inhibitor of host interferon (IFN)
production [31]. The EBOV virus VP35 protein, which plays an
essential role in viral RNA synthesis, acts as a type 1 IFN
antagonist by blocking phosphorylation of the IFN-regulatory
factor 3 (IRF3), which acts as a transcription factor for IFN
production and turns on a number of anti-viral genes [25, 27].
Figure19: From [31]

19. 19
RF-3 is activated early during virus infection by the presence of dsRNA molecules within the cell, and it acts in
conjunction with other transcription factors to turn on the expression of immediate early antiviral genes such as IFN-
α/β, IL-15, ISG15, and ISG56. It was found that a C-terminal basic amino acid motif in VP35 is required for inhibition
of ISG56 reporter gene expression as well as IFN-β production [39].
Previous studies showed that infection of 293 T cells with Sendai virus (SeV), a potent inducer of the type I
interferon system, activates the IFN-responsive promotor ISG56 in an IRF-3-dependent manner, and this activation
is significantly inhibited by the presence of VP35 from Ebola virus. In this transfection-based reporter gene assay,
293T cells were transfected with
1. ISG56-firefly luciferase plasmid (pISG56/pGL3b)
2. a VP35 expression plasmid (pCEZ-VP35), and
3. a constitutively expressed Renilla luciferase plasmid (phRG-TK) [39].
After induction of the interferon pathway by SeV infection, firefly luciferase activity was measured and normalized
relative to Renilla expression. SeV infection induced approximately a 10-fold increase in firefly luciferase activity in
control wells, and this expression was significantly inhibited by the presence of VP35 but not the ebolavirus NP
protein [39]. So if VP35 is inhibited by a particular compound in EBOV-infected cells then fluorescence emitted will
be the same as that of SeV infected cells.
Figure 20: The effect of C-terminal deletion mutations on IFN-antagonism mediated by VP35. (A) SeV induction of ISG56-
luciferase expression in the presence of an empty vector control plasmid, ebolavirus VP35, or ebolavirus NP. (B) Schematic
illustration of the 5 C-terminal deletion constructs. Full-length VP35 is illustrated on top. Stop codons were inserted at the
indicated residues. (C) Evaluation of each deletion construct in the ISG56-luciferase reporter gene assay. Error bars indicate
the average of each construct tested in duplicate; results shown here are representative of three independent experiments [39].
This study found that the 40 amino acids of the C Terminal is essential for the inhibitory activity of VP35 as
demonstrated by an experiment in which five C-terminal deletion constructs were generated by inserting a stop

20. 20
codon at the indicated position using the overlap-extension PCR method. When each of these constructs was
tested in the reporter gene assay, all five truncated proteins lost the ability to block ISG56 activation. The largest of
the proteins, R300T, has a stop codon inserted at arginine 300, resulting in a deletion of the C-terminal 40 amino
acids [39].
METHODOLOGY: [39]
293T cells were transfected in suspension by the calcium phosphate method with the following:
2 µg of pCEZ-VP35
150 ng of pISG56/pGL3b
150 ng of phRG-TK
4.4 µg of salmon testes carrier DNA
Combined plasmid DNA is diluted to 110µl in sterile water.
125 µl of 2 × HEPES-buffered saline was added, followed by 15.5 µl of 2 M CaCl2 added dropwise with gentle
shaking.
The DNA mixture was allowed to sit at room temperature for 30 min before using it to resuspend a cell pellet
containing approximately 0.5–1.0 × 106 cells.
The mixture of cells and DNA complexes was incubated at room temperature for 15 min, at which time 2.3 ml of
DMEM/10% FBS/Pen-Strep was added, and the cells were transferred to 6-well plates for incubation at 37 °
C.
Twenty-four hours following transfection, the cells were infected with 1024 HAU of Sendai virus per well.
For each well, 50 µl of virus was diluted in PBS/BA (Dulbecco's PBS w/Ca2+/Mg2++, 0.2% Bovine Albumin,
Penicillin/Streptomycin) to a total volume of 600 µl.
The media from each well was removed, and the cells were washed once with PBS before adding 600 µl of
virus mixture.
The plates were incubated at room temperature for 1 h, at which time the inoculum was removed and replaced
with 2.3 ml of DMEM containing 0.2% BA and Penicillin-streptomycin.
After 18–20 h at 37 ° the cells were harvested i n 500 µl of passive lysis buffer, and 20 µl of each sample was
C,
tested in the Dual-luciferase assay according to the manufacturer's instruction.
The firefly luciferase values were normalized to the Renilla values for each sample.
The relative fold-induction of reporter gene expression was assessed by comparing SeV-infected wells versus
uninfected control wells.
This methodology can be adapted for HTS screening of a library for compounds that effectively inhibits the activity
of VP35, as this assay specifically measures the inhibition of vp35 with regards to the particular pathway that it
inhibits.

21. 21
Illustration of the principle for the luciferase-based assay (Figure 21)
Infected with Sendai virus.
Image Taken from [40]
The firefly luciferase values are normalized to the Renilla
values for each sample.
The relative fold-induction of reporter gene expression is
assessed by comparing SeV-infected wells versus
uninfected control wells.
SeV induction of ISG56-luciferase expression [39]

22. 22
LEAD COMPOUND
Several studies have found that the Influenza virus protein NS1 has striking similarity in terms of function and
structure of the effecter domains. Like VP35, NS1 induces antiviral RNAi response in the infected host cells. VP35
has a dsRNA-binding motif with high similarity to the dsRNA-binding domain of the NS1 protein [41]. Additionally,
the NS1 protein is able to prevent viral activation of IRF-3 and NF-κB, central components in promoting type I IFN
synthesis [38]. The NS1 protein of influenza A virus blocks both the production of type I IFN and the activation of
the IFN-induced antiviral proteins PKR and OAS [41].
A bioinformatics study identified an 8-residue motif in VP35 that has 75% sequence identity to the influenza NS1A
protein, including basic residues essential for binding of dsRNA by NS1 [38]. Mutation of these residues in both
NS1 and VP35 inhibited their IFN antagonist function [38]. Therefore like NS1, VP35 inhibits phosphorylation,
activation, and nuclear localization of IRF-3 and inhibits viral- and dsRNA-induced expression of the IFNβ gene.
VP35 also inhibits activation of the cellular antiviral kinase RNA-dependent protein kinase (PKR) and activation of
the RNAi pathway [38].
Bioinformatic comparison revealed that a 9-amino acid region
(a.a. 304–312) in the C-Terminal region shows remarkable
similarity to part of the N-terminal RNA-binding domain of the
influenza A virus NS1 protein (a.a. 36–46). No other known
viral interferon antagonists showed any similarity with VP35
[39].
Figure 22: A short C-terminal motif within VP35
displays high identity with part of the N-terminal
Alanine substitution studies found that out of the three basic RNA-binding domain of influenza virus NS1 protein.
amino acids changed to alanine, the R312A mutation resulted Part of the N-terminal RNA binding domain of NS1
from influenza A/WSN/33 (M12597) compared to the
in the greatest disruption to the inhibitory capacity of VP35.
C-terminal domain from Zaire ebolavirus Mayinga
Thus, of the three amino acids studied here, R312 appeared VP35 (AF272001). Asterisks below NS1 sequence
to be the most important amino acid for inhibiting ISG56 indicate residues that have been shown to be
responsible for RNA-binding. Asterisks above VP35
promotor activation (IFN pathway) [39]. sequence are the basic amino acids changed to
alanine residues in this study [39].
Double mutations in K309A and R312A completely abolished the inhibitory activity [39]. Within the 73-amino acid N-
terminal RNA-binding domain, substitution of the highly conserved residues R38 and K41 with alanines prevented
RNA binding, destroyed some of the ability to antagonize IFN [39].
From all of these findings we can safely conclude that NS1 and VP35 are very similar and therefore a drug that can
inhibit NS1 could also theoretically have some degree of inhibitory activity against VP35.
There is currently no approved NS1 protein inhibitor in the market, but I was able to find one that had been applied
for patent ship. So, technically this inhibitor should also be able to have some activity against VP35.

23. 23
In this invention the inventors have identified small “organopharmaceuticals” that inhibit the activity of NS1 protein,
but do not affect NS1 protein gene expression. NS1 protein inhibitors typically have a molecular weight of about
500g/mol or less [42].
The inventors screened a number of compounds of which Compound 8.3 was found to be the most potent with
Compound 8.6 being the second most effective in the infection assay (Figure 23 and 24). The library that they used
for high-throughput screening constituted about 200,000 small molecules which is owned by the University of
Texas, Southwestern [42].
Figure 23: Data taken from [42]. The table depicts the compounds that were screened. Compound 8 was the most effective.

24. 24
Figure 24: Data taken from [42]. Compound 8.3 was found to be the most potent followed by Compound 8.6
SELECTED LEAD COMPOUND CANDIDATE
Figure 25: My lead compound
This is the compound that I have selected as the lead compound. Since it shows efficacy against NS1 and since
NS1 and VP35 domains are strikingly similar, I hypothesize that this organopharmaceutical would also be effective
in inhibiting VP35 and thus allowing the initiation of the IFN pathway and subsequent activation of various other
immune responses thus stopping the progression of the infection.

25. 25
LEAD OPTIMIZATION
The 3D structure of the target VP35 Interferon Inhibitory Domain is given below. The yellow portion indicates
the 40 amino acids essential for VP35 activity-residues from 300-340 [39]. The red portion indicates the three basic
residues – ARG305, LYS109 and ARG312, which are critical for VP35 to effectively block activation of an IRF-3
responsive promoter [39]. The following image (Figure 26) is taken from the RCSB Protein Database; Key word
3FKE [32].
The following is a 3D structure of VP35 inhibitory domain (shown in pink, red, blue and green showing the three
essential residues) complexed with dsRNA (shown in cyan). The PDB file is taken from RCSB Protein database;
Keyword- 3L25. [43] Figure 27:

26. 26
LEAD OPTIMIZATION & CREATION OF NCEs BY SAR STUDIES FOR AN ANTI-
LEAD OPTIMIZATION RESULTS
The lead compound that I had selected is given below
Table 1: Structural modifications of the lead:

27. 27
Since lysine and arginine are basic amino acids I have included a lot of Hydrogen bond forming groups in the
structures.
Table 2: The R1 and R2 groups of the different structures are given below:
COMPOUND R1 R2
LEAD -piperdine -(Ch3)5 - COOH
NCE (1) -piperdine - CH3-C4H9NO
NCE (2) -NO-OH -CH3-C4H9NO
NCE (3) -NO-OH -(Ch3)5 - COOH
NCE (4) - -CH3-COOH
NCE (5) -COOH -CH3-COOH
NCE (6) -NO-OH -CH3-NO-OH
NCE (7) -NO-OH -CH3-CH3
NCE (8) - -CH3-NO-OH
NCE (9) -(CH3)3-C4H9NO -CH3-NO-OH
NCE (10) -NO-OH -methylmaleic anhydride
Figure 28 Figure 29
In the figure to the left I have shown the side chains of the three residue protruding outside into the active site [32].
In the figure to the right I have shown the amino acids in the active site and how they are configured/oriented. I got
this image by using the RCSB PDB Ligand Explorer 3.7 for VP35 (Key word-3L25).

28. 28
IN VITRO SAFETY PHARMACOLOGY PROFILING
Anti-viral drugs are difficult to develop and the two broad-spectrums anti-viral compounds in the market-
Ribavirin and Interferon alpha have several side effects such as anemia, headache, irritability, anxiety, alopecia,
itchiness, insomnia, arthralgia, myalgia, anorexia, neutropenia, nausea, vomiting, fever, chills and fatigue [44].
My drug is going to be administered by intravenous injection; therefore I can hypothesize that those
problems of nausea and vomiting can be avoided. The adverse effects of my lead compound could therefore be
associated with hematology, musculoskeletal, dermatology and to certain extent maybe neurology as well.
Therefore the in vitro SPP assays that are used to screen the NCEs are as follows:
• Luciferase Reporter based gene assay [39] – Measure the binding affinity
This assay measures the inhibition of VP35 by NCE compounds in
Sendai virus (SeV) infected 293 T cells, a potent inducer of the type I
interferon system, which activates the IFN-responsive promotor ISG56 in an
IRF-3-dependent manner, and this activation is significantly inhibited by the
presence of VP35 from Ebola virus. In this transfection-based reporter gene
assay, 293T cells were transfected with
ISG56-firefly luciferase plasmid (pISG56/pGL3b)
Figure 30: SeV induction of ISG56-
• A VP35 expression plasmid (pCEZ-VP35), and luciferase expression in the presence of
an empty vector control plasmid,
• a constitutively expressed Renilla luciferase plasmid (phRG-TK) ebolaviruss VP35, OR ebolavirus NP.[39]
After induction of the interferon pathway by SeV infection, firefly luciferase activity was measured and
normalized relative to Renilla expression. SeV infection induced approximately a 10-fold increase in firefly luciferase
activity in control wells, and this expression was significantly inhibited by the presence of VP35 but not the
ebolavirus NP protein. So if VP35 is inhibited by a particular compound in EBOV-infected cells then fluorescence
emitted will be the same as that of SeV infected cells.

29. 29
• Plaque assay for Ebola virus [36] – Confirmatory assay for VP35 inhibtion by NCE
This assay is also referred to as the Neutral Red Uptake
Assay. Confluent Vero cells are infected with an EBOV strain.
After absorption of the viral innoculum for 1h, 30 ml of EBM
containing 5% FBS, antibiotics and HEPES buffer are incubated
in flasks for 10 days. Harvested medium is centrifuged and the
supernatant fluid is made into dilutions using L-15 medium and
inoculated into monolayers of cell lines being tested. They are
then treated with the different NCEs possibly in different
concentrations as well. After various incubation periods, cell
monolayers are stained using an agarose overlay containing
neutral red. Plates are then examined for plaques 24 and 48
hours after adding the stain overlay. The viral origin of the
plaques is verified by inoculating one of the plaques mixed with L-
15 medium into suckling mice. After death of the mice, the livers
are removed, processed for virus isolation, and examined for viral
antigens with the IFA procedure. Liver tissue collected from mice
which had died postinoculation will show EV-specific fluorescence
by IFA and from this the PFUs can be counted.
Figure 31: From [36]
• In vitro absorption, distribution, metabolism and excretion (ADME) assays:
ADME-Tox assays define or investigate a lead candidate’s pharmacokinetic and metabolic stability/toxicity. They
help in flagging adverse clinical effects at low cost and can prevent high attrition rates during clinical trials.[50] The
ADME-Tox assays that I have selected for screening my NCEs for are as follows:
Cytochrome P450 (CYP450) inhibition [45][46]
Anti-viral drugs have been shown to have an effect on this family of enzymes [50]. It is a
luminescence based method to measure cytochrome P450 (CYP) activity. The assay is designed to
measure the activities of CYP enzymes and test the effects of the NCEs on CYP activitiesThe CYP
enzyme substrate which are usually derivatives of luciferin is converted by CYP enzymes to a
luciferin product that is detected in a second reaction with the Luciferin Detection Reagent. The
amount of light produced in the second reaction is proportional to CYP activity.

30. 30
A.
P450-Glo™ Substrate
(proluciferin)
CYP Enzyme
O
B. R
N N O
Figure 32: taken from [46]
HO S
Luciferin Detection Reagent
Light
Human Liver Microsome Assay [47]
HLM assays are carried for investigating whether the lead compounds have any effect on as
well as for measuring UDP glucuronosyltransferase (UGT) activity. The UGT family of enzymes
are involved in the metabolism of various compounds in the body by transferring a hydrophilic
glucuronic acid moiety to their substrates, rendering them more water soluble and suitable for
excretion.
To measure UGT activity, two glucuronidation reactions are set up in parallel. Both reactions
contain a source of UGT and the proluciferin substrate, but only one of them contains the
uridine 5´-diphosphoglucuronic acid (UDPGA) cofactor. During the incubation period with the
UGT enzyme or enzymes, a portion of the proluciferin substrate is glucuronidated in the
reaction containing UDPGA. None of the proluciferin is glucuronidated in the reaction lacking
UDPGA. In the second step of the assay, incubation of the proluciferin substrates with D-
Cysteine in the Luciferin Detection Reagent results in conversion of the proluciferins into
luciferin molecules.
Luciferin produced from the unmodified proluciferin will give light in the Luciferin Detection
Reagent, but the luciferin produced from the glucuronidated proluciferin will not give light.
Therefore, the decrease in light output when comparing the plus-UDPGA reaction to the minus-
UDPGA reaction is proportional to the glucuronidation activity in the first step [47].

31. 31
OH O
N UGT HO O N
C N C N
HO S HO O S
UDPGA UDP OH
Plus D-Cysteine
OH O O
O
HO N
N O N OH
N OH
HO O S S
S S
HO
OH Figure 33 taken from [47]
Plus Luciferin Detection Reagent
Light No Light
7984MA
Figure 33:. Conversion of UGT Multienzyme Substrate by UGT enzymes. UGT enzymes attach a glucuronic acid
moiety to the proluciferin substrate. During the detection step, the proluciferin is simultaneously converted to a luciferin
by cyclization with D-Cysteine. Luciferase uses the luciferin analog of the initial substrate to produce light but does not
produce light with the glucuronidated luciferin. Light output is inversely proportional to UGT enzymatic activity.[47]
hERG Potassium Channel Screening
The protein product of the human ether-a-go-go gene
(hERG) is a potassium channel that when inhibited may lead
to cardiac arrhythmia [48]. Prediction of the hERG affinity
value, QT prolongation, and action potential parameters are
recommended as test criteria by the FDA [49]. RLB assays
are commonly used as primary screens for hERG inhibition,
whereas patch clamp analysis remains the gold standard
[50].
Planar patch clamp is the one that I have selected for
Figure 34:The cell-attached patch clamp uses
measuring hERG liability because it allows for a multiwall
a micropipette attached to the cell membrane to
format and automation, which is much faster and less labor
allow recording from a single ion channel [51].
intensive [49].
Patch clamp technique which is a refinement of the voltage clamp allows the study of ion channels in
cells. Patch clamp recording uses, as an electrode, a glass micropipette , a size enclosing a membrane
surface area or "patch" that often contains just one or a few ion channel molecules. The interior of the

32. 32
pipette is filled with a solution matching the ionic composition of the bath solution, as in the case of cell-
attached recording, or the cytoplasm for whole-cell recording. A chlorided silver wire is placed in contact
with this solution and conducts electrical current to the amplifier. The investigator can change the
composition of this solution or add drugs to study the ion channels under different conditions. The
micropipette is pressed against a cell membrane and suction is applied to assist in the formation of a
high resistance seal between the glass and the cell membrane [51].
In case Planar patch clamp assay, cell suspension
(containing a single cell randomly chosen by
application of suction) is pipetted on a chip
containing a microstructured aperture. A single cell
Figure 35. The patch pipette is moved to the cell using a
is then positioned on the hole by suction and a tight
micromanipulator under optical control. The cell is then
connection (Gigaseal) is formed. The planar
positioned by suction. [51]
geometry offers a variety of advantages compared to
the classical experiment:
• it allows for integration of microfluidics, which
enables automatic compound application for ion
channel screening.
• the system is accessible for optical or scanning
probe techniques
• perfusion of the intracellular side can be performed
[51, 52].
Figure 36: (A)Procedure of cell contacting. (B)Measured
current response to a voltage pulse and after a cell is sealed
onto the aperture by suction (C) Close-up view of the
mechanically and electrically tight contact of the cell
membrane and the chip in cell attached mode [51]

33. 33
IN VITRO SPP PROFILE RESULTS
Table 3:
VP35 Inhibition Assays ADME-Tox Assays
NCE ST 1: VP35 ST2: PLAQUE ST3: hERG ST4: CYP 450 ST5: UGT
INHIBITION, ASSAY(confirmatory INHIBITION INHIBITION ACTIVITY
LUCIFERASE assay for VP35 (Planar patch ASSAY ASSAY
BASED GENE inhibition) clamp assay) (Human Liver
ASSAY IC50 (µM) Microsome
PFU IC50 (µM) assay)
IC50 (µM)
IC50 (µM)
NCE (1) 5.3 3.8x103 6.8 7.6 2.2
NCE (2) 3.4 103 8.9 8.2 7.0
NCE (3) 2.3 100 >10 >10 9.1
NCE (4) 9.1 5.4x103 3.0 2.9 2.2
NCE (5) 4.1 1.2x103 7.2 7.6 8.1
NCE (6) 4.2 2x103 5.6 5.2 5.0
NCE (7) 7.0 4.5x103 4.1 4.7 4.9
NCE (8) 7.5 5x103 4.6 5.0 5.1
NCE (9) 2.1 75 >10 >10 >10
NCE (10) 3.9 3.1x103 6.2 5.6 6.7

34. 34
CONCLUSION
I hypothesize that NCE (9) is the best as:
• It is functionalized with hydrogen bond forming groups that could engage the basic amino acids ARG305,
LYS109 and ARG312, which are critical for VP35 to effectively block activation of an IRF-3 responsive
promoter.
• It has got good inhibitory activity that is evident from the IC50 values of the luciferase reporter based gene
assay and plaque assay.
• It has got a safe ADME-pharmacokinetic profile that is evident from the ADME-tox (In vitro SPP) assays.
The second best is NCE (3).
NCE (9) is going to be referred as NCT 1087 in future studies.

35. 35
PATENT APPLICATION
A standard patent application for NCT1087, a VP35 protein inhibitor with the potential to act as an anti-ebola small
molecule drug will be filed with the United States Patent and Trademark Office (USPTO).
ABSTRACT
Compounds in the present invention inhibit the activity of VP35 protein, thereby mitigating Ebola Viral infection as
VP35 is critically involved in its pathogenesis. The compounds, the method of use and formulation is included in this
patent.
Compound being patented:
• NCE-9 also known as NCT1087
• NCE-3
• NCE-2
• NCE-5
NCT1087 shows the maximum potency as a VP35 inhibitor. The other compounds show comparable potency.
Therefore they will also be patented to slow down potential competition.
Background of the invention:
Ebola hemorrhagic fever is a severe, often-fatal viral hemorrhagic disease in humans and nonhuman primates that
has appeared sporadically since its initial recognition in the Democratic Republic of Congo in 1976 [1]. It is caused
by the Ebola Virus which interferes with the interior endothelial cell lining of blood vessels and coagulation which
leads to hypovolemic shock [2]. Destruction of endothelial surfaces is associated with disseminated intravascular
coagulation, and this may contribute to the hemorrhagic manifestations.[5] Fatality rate differs from 50-83% [2]. To
date, beyond supportive care, no effective treatments, therapies, or vaccines are approved to treat or prevent Ebola
virus infections because natural immunity to this infection is difficult to find, plus there are no immune correlates in
humans [10].
Summary of the invention:
The present invention has identified small organopharmaceuticals that can inhibit VP35, a major virulence factor in
EBOV infection. It can be hypothesized that EBOV infection can be treated by administering an effective amount of
compound NCT1087.

36. 36
SELECTION OF APPROPRIATE ANIMAL MODELS FOR EVALUATING THE
EFFICACY OF THE ANTI-EBOLA DRUG
In order to effectively evaluate the efficiency of the lead compounds in halting the progression of the disease
through inhibition of VP35, we need an animal model that can accurately represent the pathogenic mechanisms
that underlie EHF.
The three widely used animal models in Ebola research are mice, guinea pigs and NHPs with EHF being
best reproduced in NHPs. There are several disadvantages associated with the use of rodent models and these
are: [27]
• Wild type EBOV is not lethal in them.
• EBOV strains have to be adapted to these models through specific mutations in NP and VP24.
• Some aspects of the human form of the disease cannot be authentically replicated such as the
haemorrhagic manifestations.
• There is considerable difference in rodent and human immunology.
• Bystander apoptosis of lymphocytes, which is observed in humans, is not prominent in rodents.
• a number of antiviral therapies and vaccines that were effective in mice failed to protect nonhuman
primates. [53]
Table 4: Comparison of animal models with the human disease [27][54]
Mouse Guinea pig NHP Human
Adaptation
Yes Yes No No
required
Macular rash No No Yes Yes
Haemorrhagic
Not profound No Yes Yes
manifestations
Coagulation
Not profound Conflicting data Yes Yes
abnormalities

37. 37
Mouse Guinea pig NHP Human
Liver enzymes Elevated Elevated Elevated Elevated
Thrombocytopen
Yes Yes Yes Yes
ia
Bystander
No No Yes Yes
apoptosis
Cytokine
Yes Yes Yes Yes
response
Time to death 4–6 days 6–9 days 6–9 days 6–16 days
Required
infrastructure Moderate Moderate Very high NA
and/or costs
Ethical concerns Moderate Moderate High NA
Monocytes, Monocytes,
Monocytes, macrophages, macrophages,
Monocytes,
macrophages, dendritic dendritic cells, dendritic cells,
macrophages, dendritic
Permissive host cells, fibroblasts, fibroblasts, fibroblasts,
cells, fibroblasts,
cells hepatocytes, adrenal hepatocytes, hepatocytes,
hepatocytes, endothelial
cortical cells, endothelial adrenal cortical adrenal cortical
cells, epithelial cells
cells, epithelial cells, endothelial cells, endothelial
cells, epithelial cells, epithelial
Cytokines/chem
okines IFN-a, IL-6, IL-18,
IFN-a, IL-2, IL-6, IL-10,
(increased MCP-1, TNF-a NE MIP-1a, MIP-1b,
TNF-a
circulating MCP-1, TNF-a
levels)
The only drawback with using NHPs is that the typical time of death is 6-9 days after exposure to ZEBOV infection,
whereas in humans the time of death is prolonged which might be due to an adaptive immune response which is
not seen in NHPs. However this doesn’t matter much in the drug that I will be testing as its primary function is to
activate the innate immune system through initiation of the type I IFN pathway. In addition, experimentally infected
NHPs are normally exposed to higher doses of EBOV than humans would be during a natural exposure [27].

38. 38
Because of the ethical issues associated with the use of NHPs for research, I would first like to evaluate the efficacy
of the NCEs on a mouse model and then proceed testing the promising candidates using a primate model.
MOUSE MODEL USED FOR PRECLINICAL STUDIES (Efficacy evaluation)
The most commonly used mouse strains for EHF research are:
• BALB/c mice [55]
• SCID mice [56]
• ICR (CD-1) outbred mice [57]
The Ebola VP35 protein is multifunctional, acting as a component of the viral RNA polymerase complex, a viral
assembly factor, and an inhibitor of host interferon (IFN) production [31].
Therefore in my initial study with mouse models, SCID mice will be used in initial drug evaluation studies to gauge
the lead compound’s ability to inhibit viral replication independent of immunological factors.
Then in the second phase of the Mouse preclinical studies, adult, immunocompetent BALB/c mice will be used to
evaluate the efficacy of the lead compound in inhibiting the VP35 antagonism of Type 1 IFN pathway.and thus see
if this leads to increased expression of antiviral genes and subsequent immune cell clearance of the virus.
Figure 37- Image taken from [58] **Image taken from [59]

39. 39
The adaptation of EBO-Z to mice passaging intracerebrally in suckling mice, then in Vero cells and finally by
subcutaneous or i.p. inoculation in progressively older suckling BALB/c mice. Virus recovered from the liver of a
moribund ninth-passage mouse was plaque-purified twice and amplified. This ‘mouse-adapted virus’ is lethal for
adult BALB/c and other mouse strains when inoculated i.p. The 50% lethal dose (LD50) is 0.03 plaque-forming units
(pfu), or approximately one virion [60].
Adult SCID and BALB/c mice will be divided into four groups:
• Control
• EBOV infected (Negative control group)
• EBOV infected treated with NCE at one concentration
• EBOV infected treated with NCE at a different concentration.
Infection will be done by inoculatiion (i.p.) with 1000 pfu (30 000 LD50) of mouse-adapted EBO-Z. Negative control
groups can be treated with a placebo (PBS) or left as such [61].
Parameters checked for in the animal models:
In case of the SCID mice group:[60]
• serum viral titer levels will be examined every day postinfection.
In case of BALB/c mice group: [60][61]
• Serum cytokine concentrations of IFN-α, macrophage chemotactic protein-1 (MCP-1), interferon-gamma
(IFN-γ) and tumor necrosis factor-alpha (TNF-α) will be measured using commercial kits.
• Liver and spleen of infected and uninfected mice will be examined by Immunohistochemistry and Electron
microscopy so that we can study the effect of the NCE on the progression of the infection in major target
organs.
An experiment we can do to support my hypothesis that the NCE elicits its effect by way of the type I IFN pathway
is by co-administering antibodies to interferon alpha/beta. This will eliminate the efficacy of the drug that it mediates
via the IFN pathway. This will prove beyond doubt that the NCE acts by inhibiting VP35 and subsequent activation
of the IFN pathway. We can again confirm this by comparing the production of IFN-α in Ebola virus-infected mice
treated with the NCE or with placebo. [61]

40. 40
NON-HUMAN PRIMATE MODEL USED FOR PRECLINICAL STUDIES
EBOV has been shown to cause fatal hemorrhagic manifestations in: [57][53]
• Rhesus macaques ( Macaca rhesus )
• Cynomolgus macaques ( Macaca fascicularis )
• African green monkeys ( Cercopithecus aethiops)
• Baboons ( Papio hamadryas )
• Vervet monkeys ( Cercopithecus aethiops )
These are the NHP models most commonly used for Ebola research as they accurately replicate the clinical
manifestations of EHF in humans. I will be choosing a combination of Rhesus and Cynomolgus macaques for the
preclinical testing of my NCEs as these two models have been the most widely used NHP model for EBOV
research.
Figure 37 -Representative cutaneous
rashes from cynomolgus monkeys
experimentally infected with EBOV-
Zaire. A: Characteristic petechial rash
of the right arm at day 4.B: Petechial
rash of the inguinal region at day 5.
Image taken from [62].
Figure 38. Rhesus monkey
infected with Ebola virus showing
an extensive rash on the face and
anterior aspects of the arms [63].

41. 41
As in the case of mouse models the NHPs will be divided into three groups:
• Control
• EBOV infected (Negative control group)
• EBOV infected treated with NCE at a concentration defined in the mouse model study.
Infection will be done by inoculation (i.p.) with 1000 pfu (30 000 LD50) of EBO-Z. Adaptation of the EBOV strain is
not required. EBOV from a fatally infected patient can be directly used. [62] Negative control groups can be treated
with a placebo (PBS) or left as such.
Parameters checked for in the animal models:
• Cytokine/chemokine levels of interleukin (IL)-2, IL-4, IL-10, IL-12, interferon (IFN), tumor necrosis factor
(TNF), IL-6, IFN-α, IFN-ß, MIP-1, MIP-1ß, IL-1ß, IL-8, IL-18, and MCP-1 in monkey sera/plasma can be
assayed using commercially available ELISA kits. (generally their levels should have increased in treated
models) [62][64].
• Nitrate levels were determined using a colorimetric assay. (reduction should be seen in treated models)
[62][64].
• Viral titer levels will be determined every day post infection. (reduction should be seen in treated models).
• Necropsy will be performed on the models. Tissue samples of the liver, spleen and the lung were collected
from each monkey for histopathological, immunohistochemical, in situ hybridization examination as well as
electron microscopy examination [62][64].
• Total white blood cell counts, white blood cell differentials, red blood cell counts, platelet counts,
total hemoglobin concentration will be determined to account for bystander apoptosis which is a common
manifestation of EBOV infection [64].
• Concentrations of albumin (ALB), amylase (AMY), alanine aminotransferase (ALT), aspartate
aminotransferase (AST) will be analyzed as AST and ALT levels are found to be elevated during EBOV
infection. So there should be a reduction in their levels in treated models [64][65].
• Plasma levels of fibrin degradation products (D-dimers) will be analyzed using ELISA as they are found to
decrease during the infection [64],

42. 42
BIOMARKERS
Biomarkers in the context of a viral infection are biological molecules associated with a disease caused by
an infectious viral agent. They are essential in diagnostic and therapeutic processes as they: [66][76]
• Enable early diagnosis
• Reduce risk in drug development
• Improve patient outcomes
• Patient stratification
• Assessment of drug toxicity and efficacy
• Disease staging
• Disease prognosis
• Guide molecularly targeted therapy
• Monitor the activity and therapeutic responses across a variety of diseases.
Figure 39: Left: Disease pathway and potential impact of biomarkers. Image taken from [67] Right: .Biomarker
science is a multifaceted discipline which impacts all aspects of drug development and modern medicine. Image
taken from [81]

43. 43
Figure 40: Biomarker discovery and application as an integral component of drug development. (a) Disease
program approaches should yield biomarker candidates. (b) Parallelism of biomarker development in the drug
development pipeline. Biomarkers can be applied to many steps in the drug-discovery pipeline. They can also be
evaluated for use in both a pre- and post-market follow-up study. Image taken from [82].
DISEASE BIOMARKERS
There are essentially three kinds of disease biomarkers:
1. Disease Trait- is essentially a biomarker of exposure that is used to calculate the risk of exposure,
that is the likelihood that an individual is susceptible to a particular disease. [67] The likelihood of
getting Ebola hemorrhagic fever is not governed by any genetic factors. Therefore this disease doesn’t
have a disease trait biomarker as every segment of the population is equally susceptible to it.

44. 44
2. Disease State- is a biormarker used for diagnostic purposes. The potential uses of this biomarker is
the [67]
• identification of individuals who will be or are in the preclinical stages of the disease.
• reduction in disease heterogeneity in clinical trials.
• reflection of a disease pathogenesis that is the phase of induction, latency and
detection.
• target for a clinical trial.
Table 5: Biomarker for diagnosis and typing of Ebola Hemorrhagic Fever [68]
Validated Potential
Detection/Diagnosis Glycoprotein (GP) VP24
Nucleoprotein VP30(minor
GP gene nucleoprotein)
NP gene VP35 (P-like protein)
VP40 (Matrix Protein)
VP24 gene
VP30 gene
VP35 gene
VP40 gene
Pathogen Typing GP gene
Virulence Factor Glycoprotein (GP)
3. Disease Rate - This biomarker is used to indicate or evaluate the stage of the disease. It can also be
referred to as a prognostic biomarker [84]. In case of ebola hemorrhagic fever it will be the viral titer
that is copies of EBOV/ml of blood or serum.

45. 45
SURROGATE BIOMARKER
“A surrogate biomarker is defined as a biomarker intended to substitute for a clinical endpoint, the latter
being ‘a characteristic or variable that reflects how a patient feels, functions, or survives” [69].
In case of Ebola Hemorrhagic Fever, hypotension, generalized fluid distribution problems, lymphopenia,
coagulative disorders, and hemorrhages are its characteristic features [70]. In Ebola-infected patients,
there is extensive apoptosis of leukocytes which is associated with the fatal outcome of the disease. This
observation appears consistent with considerable lymphopenia and severe damage to lymphoid tissues,
such as spleen, lymph node and bone marrow, seen in patients and experimentally infected monkeys
[71].
Therefore the surrogate marker that I have selected is the level of lymphocytes in the blood which will
progressively decrease with disease pathogenesis and will increase with a therapeutic intervention.
TOXICITY BIOMARKERS
These biomarkers are used to monitor the adverse effects of a specific drug on any unintended cellular
processes, cells, tissues or organs [84].
RENAL TOXICITY
Due to the possible renal side effects of my NCE, the following nephrotoxic biomarkers which has been
approved by the FDA will be used to monitor the patients during the treatment period [72][73].
• Serum creatinine
• Blood urea nitrogen
• Glomerular filtration rate
HEPATIC TOXICITY
Pro-inflammatory cytokines such as:
• tumor necrosis factor alpha (TNFalpha),
• interleukin 1beta(1L-1beta)
• and interleukin 6 (IL6)
are involved in acute and chronic liver damage. They are released both from the liver and from distal sites
during hepatic toxic injury [74]. These cytokines are also involved in disseminated intravascular

46. 46
coagulation (DIC), which is a prominent manifestation of Ebola virus (EBOV) infection. DIC is a syndrome
characterized by coagulation abnormalities including systemic intravascular activation of coagulation
leading to widespread deposition of fibrin in the circulation, which contributes to the multiple organ failure
and high mortality rates characteristic of EBOV infections [70].
Alternatively alanine transaminase and bilirubun could be used as a measure of liver toxicity [75].
TARGET BIOMARKER
A target biomarker is used to report the interaction of the NCE with the target. The Ebola VP35 protein is
multifunctional, acting as a component of the viral RNA polymerase complex, a viral assembly factor, and
an inhibitor of host interferon (IFN) production [77]. The EBOV virus VP35 protein, which plays an
essential role in viral RNA synthesis, acts as a type 1 IFN antagonist by blocking phosphorylation of the
IFN-regulatory factor 3 (IRF3), which acts as a transcription factor for IFN production and turns on a
number of anti-viral genes such as IFN-α/β, IL-15, ISG15, and ISG56 [78][79].
Inhibition of VP35 by the NCE will result in the phosphorylation of IRF3 that forms a complex with
CREBBP that translocates to the nucleus and activates the transcription of the different anti-viral genes;
therefore IRF3 or phosphorylation of IRF3 will be the target biomarker [86].
MECHANISM BIOMARKER
Mechanism biomarker is a biomolecule associated with a specific pathway that gets affected by the drug
and brings about the desired clinical effect. In case of Ebola hemorrhagic fever, the NCE will inhibit VP35
bringing about the phosphorylation of IRF3. This leads to the transcriptional up-regulation of type I IFN,
IFN-α, IFN- γ and IFN-β, genes. This signaling stimulates transcription of IFN-sensitive genes, including a
number that encode antiviral proteins, and leads to the induction of an antiviral state. Among the antiviral
proteins induced in response to type I IFN are dsRNA-dependent protein kinase R (PKR), 2′,5′-
oligoadenylate synthetase (OAS), and the Mx proteins [80].
So the mechanism biomarker for the EHF will be IFN- α, IFN- γ and IFN-β. IFN- γ is indicative of the
adaptive immune system getting activated [85].

47. 47
EFFICACY BIOMARKER
Efficacy biomarkers are used to predict a patient’s response to a drug [81]. They essentially monitor the
beneficial effects of a specific drug on the intended drug target or medical condition [84]. In case of EHF,
the efficacy biomarker will be the viral load in the patient’s blood. It should decrease if the drug is effective
which is indicative of its efficacy.
TRANSLATIONAL BIOMARKER
Translational biomarker is a bridging biomarker that can be used in multiple species and can be used to
translate the results from preclinical animal studies to clinical human studies i.e. directly link responses
between species and follow such injury in both preclinical and clinical settings [83].
In case of EHF, translational biomarkers can be several things such as:
• viral titer
• interferon (IFN-α and IFN-ß) levels
• interleukin (IL-2, IL-4, IL-10, IL-12) level
• tumor necrosis factor levels
STRATIFICATION BIOMARKER
Stratification biomarker is used to identify patients likely to respond to a specific drug or suffer from its
side-effects prior to administration of the drug [84]. Since the NCE targets VP35, therefore one of the
stratification biomarkers as follows:
• presence of EBOV infection so that the drug can target VP35
• the patient must be immunocompetent as the drugs works by removing the block imposed by the
virus on the initiation of the innate and adaptive immune system. Therefore the second stratification
biomarker would be the presence of functional type I IFN genes as well as IRF3.

48. 48
EFFICACY STUDIES FOR MINIMUM EFFECTIVE DOSE
Table 6:
ANIMAL NO. OF NCT108 EFFICAC SURROG TARGET MECHANISM EFFICACY
MODELS ANIMA 7 Y BM- ATE BM- BM- IRF3 BM- IFN- γ ENDPOINT (
LS CONC. VIRAL LYMPHO CONC. CONC. No. of
(mg/kg) TITER CYTES (% animals
(pfu/ml) CONC. (% activation (p recovered
total ) g/ from EBOV
cells) ml infection)
)
0/2
SCID 2 Placebo 1.3 x 109 5% 0.1 <100
1/4
SCID 4 1mg/kg 4.8 x 105 10% 11 800
3/4
4 2 mg/kg 5.2 x 104 18% 45 1200
4/4
4 4 mg/kg 2.2 x 102 35% 65 2000
0/2
BALB/c 2 Placebo 4.1 x 1010 3.5% 1 <100
2/4
BALB/c 4 1 mg/kg 2.3 x 105 12% 12 900
4/4
4 2 mg/kg 1.4 x 103 22% 56 1300
4/4
4 4mg/kg 102 40% 75 2500
Rhesus 0/2
2 Placebo 2 x 109 6% 1.2 <100
Monkeys
Rhesus 2/4
4 1 mg/kg 3.4 x 105 13% 14 780
Monkeys
4 2 mg/kg 1.3 x 104 20% 57 1500 3/4