FUSION PROTEINS: APPLICATIONS AND CHALLENGES - Fusion Protein Technologies for Biopharmaceuticals: Applications and Challenges - page 5

the novelty. If we focus on the scope of this topic, the fusion
proteins, novelty still seems to be easy to reach. As described
in the paragraph about definitions, “joining two or more genes
by genetic engineering that originally code for separate
proteins,” so the generated fusion protein will be novel if
nobody did the same earlier. Therefore, novelty is given on
one hand through the composition of matter (the new
construct, e.g., long-acting human growth hormone [hGH],
consisting of hGH fused to human serum albumin [HSA]) or
on the other hand by the use that results from combined
features of the new molecule (e.g., to treat dwarfism with
longer administration intervals). This is in contrast to a natural
polypeptide with multiple functions [17].
Taking the example of antibodies as molecules, their
individual characteristics, for example, target or captured
epitope, affinity, half-life, or sequence of the variable part
should be sufficient to enable patenting based on novelty [18].
Surprisingly, exactly these descriptive features are missing in
many antibody patents, which is an effect of patenting human
genes that often include hypothetical antibodies to that target
in the claims [19]. It might be easier trying to patent antibodies
based on unexpected advantages, that is, having lower cross-
reactivity since higher affinity could be regarded as obvious
[20]. This should be taken into account for patenting antibody
derived fusion proteins. Particularly, tumor-specific antibod-
ies have had only limited success so far. This led to new
intellectual property of improved molecules by coupling
antibodies to toxic proteins, thus combining target specificity
with nonspecific cytotoxicity [21].
However, if we continue with the second parameter, the
nonobviousness, it starts to get more difficult. In the context
of fusion proteins in many cases, the existence or function-
ality of the potential fusion partners will be well known; thus
representing prior art. Interestingly, when combining several
“prior arts” into a new concept, this patent will only be
rejected as obvious if there existed at the time of invention a
known problem for which there was an obvious solution
encompassed by the patent's claims [22]. The best argument
to get a combination patent is to demonstrate that prior art is
not providing a motivation or suggestion to prepare this
combination. Even when sufficient suggestions for combi-
nations can be found in prior art, patenting can still be
possible if enabling in form of a production method can be
claimed additionally. Therefore, when defining patent
claims, it can be very beneficial to include methods how
to manufacture the protein of interest and what formulations
are useful [23].
The third parameter to demonstrate utility is relatively
straightforward since the fusion protein was designed with a
specific application in mind. Here, both typical aspects of
utility, recognition of a benefit and the motivation to make a
change to current practice, come into play. Overall it has to
be described how the invention can be put into practice,
which is ideally done in the form of examples.

In the past, some patent disputes ranked around pro-
tected fusion protein technology. For instance, Zymoge-
netics accused Bristol-Myers Squibb (BMS) to infringe
their Fc-fusion technology with Orencia 1 . Initially, the
case was settled by a lump sum payment, but finally BMS
acquired Zymogenetics in 2010 together with the rights for
Fc fusions [24].

1.4 DESIGN AND ENGINEERING

In the design of a novel fusion protein a number of parame-
ters have to be taken into account. Following questions need
to be addressed: Will the proteins be functional on either the
N-terminus or the C-terminus? In which orientation will the
individual proteins be connected? What linker length and
sequence should be used? Is there a need for a specific
oligomerization? Are mutations or truncations required to
enhance or eliminate certain features? In many cases rational
design will guide the generation of innovative protein ther-
apeutics [25]. One of the aims of protein design is certainly
to improve the functionality of biological drug (Figure 1.3).
A key question in this context is: Will the protein reach the
target in a significant quantity? Taking the example of a solid
tumor it becomes clear that in order to reach the tumor the
protein has to be sufficiently small to penetrate the many cell
layers. But on the other hand it should not be too small to be
excreted too fast. This requires a delicate balancing of the
molecule size and has been demonstrated experimentally
with a number of different antibody derivatives [26]. Not
only size but also valency of antibodies can be modified.
Further details on bi-specific and multifunctional antibodies
can be found in Part IIIb of this topic.

1.4.1 Orientation of Fusion Proteins

Looking at the largest group, the Fc-fusion proteins, it is well
known that naturally the Fc part is positioned at the
C-terminus of an antibody. But in artificial fusions it can
also form the N-terminal part. Several studies have evaluated
cytokine mono- or tandem fusions to full antibodies or
Fc parts. Here no dependency on the selection of the respec-
tive terminus could be observed [27]. However, comparing
N- or C-terminal Fc fusions of peptides blocking angiopoie-
tin-2 (Ang-2), it was found that the N-terminal fusion had
shorter half-life andweaker binding but better selectivity [28].
Generally, when combining two proteins, there are two
orientations in which the fusion partners can be arranged,
either at the amino or at the carboxy terminus of the first
protein. In many cases the position is without influence on
the functional properties, for instance albumin (HSA) can be
fused to either end [29]. But during the manufacture of
Albuferon 1 , a combination of interferon- a 2b (IFN- a 2b)
with albumin,

it was observed that due to incomplete