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The benefits of constructing leads from
fragment hits
‘Fragments’ refer to particularly small molecular starting points in medicinal chemistry. The small size of fragments
requires adapted techniques for their screening and subsequent elaboration. The detection of the weak binding
affinity of fragments for their target, and associated screening issues, have been debated at length. Since it is now
clear that fragments can be developed into clinical candidates, the discussion is shifting to the design of good-quality
lead compounds from fragment hits. The increasing ability to control and tailor this construction process highlights
the potential benefits of fragment-based drug discovery.
Keywords: computational chemistry n de novo n drug design n fragment n hit-to-lead
A recent but validated strategy
In the past decade, fragment-based drug discovery (FBDD) has become an established strategy
to discover medicinal lead compounds [1–5] .
These fragments (sometimes called ‘scaffolds’ [6])
are small molecules (Figure 1) , typically with a
molecular mass < 300 [7] . There is currently
much interest and investment in FBDD in both
academia and industry [2,4,8,9] , in particular
since FBDD offers several potential advantages
to develop well-tailored and high-quality lead
compounds. Indeed, FBDD has already delivered
clinical candidates [10,11] .
The specificities and advantages of fragment
screening, in particular regarding increased sampling of chemical space, have been discussed at
length [1,12] . Here, the hit-to-lead (H2L) process
when starting from fragment hits is considered, based on practical experience of FBDD at
Vernalis [2,13,14] and other reports. The article will
try to discern, in very broad terms, what may be in
general the opportunities and issues associated to
FBDD during H2L. For more extensive coverage
of the field and detailed case studies, the interested
reader is referred to recent reviews [1,2,4,8–10,15] .
hits is much less a drawback with FBDD than
HTS. Instead, H2L with FBDD can concentrate
more quickly on questions of chemical novelty
and molecular design. A key aim of H2L on a
fragment hit is to evaluate if its potency can be
quickly and dramatically optimized, alongside
other relevant properties.
The function of H2L
The identification of an early H2L phase during drug discovery emerged initially as the need
to confirm and evaluate the hits yielded by
high-throughput screening (HTS), especially
regarding compound structure and purity [16] .
However, since FBDD can operate with much
smaller screening compound collections, these
compounds can be subjected to upfront quality
control. Therefore, the chemical integrity of the
The fundamental advantages of
fragments compensate for their low
binding affinity
The small size of the fragment starting points
means that they form limited contacts with
their biological target, and, consequently, have
relatively low binding affinities. Thus, screening assays need to be able to detect this low
affinity and frequently rely on biophysical techniques, such as NMR [17] , surface plasmon resonance [18,19] , isothermal titration calorimetry [20]
or x-ray crystallography [6,21] . It is preferable
to confirm binding to the target by more than
one method [14] . Competition experiments can
reduce the list of hits to those that bind to a site
of interest. The counterpart of the low binding
affinities of fragments is that they have a greater
chance than larger molecules to form favorable
interactions complementary to a receptor binding site, without interaction mismatches [22] .
Consequently, fragment screens tend to yield a
relatively high hit rate, of course modulated by
the target druggability [23] .
Thus, FBDD can offer a broad range of diverse
starting points for subsequent medicinal chemistry. So, the H2L process starts with a triage
of the hits according to their scope for further
progression. The criteria used for this assessment
10.4155/FMC.11.46 © 2011 Future Science Ltd
Future Med. Chem. (2011) 3(9), 1111–1115
N Foloppe
Vernalis (R&D) Ltd., Granta Park,
Cambridge, CB21 6GB, UK
Tel.: + 44 1223 895 338
Fax: + 44 1233 895 556
E-mail: [email protected]
ISSN 1756-8919
Commentary | Foloppe
Fragment bound to Hsp90 (x-ray structure)
Clinical candidate in Phase II
Figure 1. Schematic illustration of the potential of fragments for their development in
clinical candidates. The top section shows examples of fragments, which were found to bind to
the ATP-binding site of the Hsp90 protein (an oncology target) at Vernalis R&D Ltd [44] . These small
molecules are representative of the small size of fragments. Accordingly, these compounds had
weak binding affinities for Hsp90. However, visualization of the fragment-binding modes to the
protein, combined with molecular modeling and medicinal chemistry, led to the progress of a
fragment hit into a potent lead compound, which is now in phase II clinical trials.
Hsp90: Heat shock protein 90.
include chemical novelty, binding affinity and
ligand efficiency (LE) [24] , whether the binding
mode to the target can be visualized, amenability to synthetic chemistry, and, sometimes, clues
of a functional profile (e.g., agonist or antagonist [11]). The weighting of these criteria is, of
course, context dependent.
The selected fragment is intuitively seen as the
core of its derived chemical series, therefore, its
novelty affects the patentability of derived analogs, especially with target classes for which an
intellectual property niche is at a premium. The
LE for such a core is another important parameter, since a high initial efficiency indicates that
the starting fragment makes very favorable interactions with the target, normalized with respect
to its number of nonhydrogen atoms. The LE of
the initial fragment influences the LE achieved
by derived analogs [25] . A high starting LE is preferred because it signals the opportunity to obtain
high-affinity lead compounds without adding
undue molecular mass, offering a promising start
towards oral bioavailability of the derived lead [26] .
Future Med. Chem. (2011) 3(9)
Accelerating H2L with
structural information
Since most fragments hits have low binding affinities, a first challenge is to increase their affinity
substantially, on a pragmatic timescale. This process is greatly facilitated in view of the fragmentbinding mode to its target, usually ascertained
by x-ray crystallography [6,11,13,15,19,21,27–30] . The
structure of the bound fragment accelerates the
H2L process since it helps to prioritize among
an otherwise very large number of elaboration
options, including those with respect to target
selectivity [11,30] . Such structure-guided elaboration assumes that the initial binding mode of the
fragment is robust and not prone to changes upon
derivatization. This requirement is frequently
met, especially when the fragments forms asymmetrical polar interactions with the receptor. Yet,
counter examples have been described [19,28,31,32] .
One may argue that alteration of a binding mode
with different substituents only adds to the range
of options for H2L progression. In our experience, binding mode switches do not typically
future science group
The benefits of constructing leads from fragments hits
hamper progress, confirming that FBDD lends
itself to a controlled constructive approach for the
design of lead compounds.
The structure-based construction of leads
from ideally positioned starting points gives the
opportunity to tailor those leads for the target
from the outset of H2L. Monitoring changes in
LE at each step helps select the most efficient substituents for binding, to increase binding affinity
while keeping the compound size under control.
Smaller compounds tend to have more favorable
absorption and distribution properties [26] . Other
relevant physicochemical properties, as well as
the selectivity profile, can be monitored and
influenced incrementally when building from
fragment to lead. Indeed a small (unencumbered)
starting point offers, in principle, the opportunity
to follow an optimal path from hit to lead. The
fragment-binding mode gives early indications
regarding which bond vectors will be engaged
in optimization of binding affinity, and which
vectors are amenable to more diverse variations to
tune overall physicochemical properties.
Thus, H2L with FBDD contrasts with situations where one is faced with a relatively large
hit with mediocre LE, where much effort may
be spent redesigning the starting point before
productive optimization can be tackled. With
HTS hits, an objective of H2L can be to find the
minimum active fragment in a complex molecule [16] . Instead, FBDD starts immediately from
a suitable core with a promising binding mode
and can concentrate more directly on the path
to a lead with well-balanced physicochemical
properties for druglikeness [4] .
Explore & design with
computational chemistry
Seeing how a fragment binds to its target gives
a helpful first impression. However, to be most
productive, FBDD can exploit the full range of
drug-design tools available from modern computational chemistry. When applicable, one
spontaneously overlays and visualizes the bound
fragment with other, larger, compounds binding
to the same site. Larger compounds will typically extend to regions of the binding site not
occupied by the fragment; hence, one naturally
tries to transfer elements from the larger compound to substitute the smaller fragment. For
this to work, the exchanged covalent bonds need
to be well aligned in a precise local overlay, and
the associated intramolecular effects must also
be compatible. These constraints make merging between compounds more difficult than
future science group
| Commentary
it appears, but there are examples of hybrid
compounds evolved from a fragment [9,13] . The
combinatorial hybridization of overlaid ligands
has been implemented in the BREED algorithm [33] . It assumes that the binding mode of
several (many) potent compounds is available;
computational docking can help obtain this
information quickly for elaborated compounds
reported in the literature, without always having
to synthesize and crystallize them.
Another tactic is to enumerate virtual libraries around the fragment core, according to predefined chosen chemistries and with accessible
reagents. Then, the virtual library can be docked
to the binding site, while enforcing the experimentally determined binding mode of the fragment core [6,11] . This explores the conformations
of the putative substituents around the fragment
core and their molecular recognition interactions
with the receptor. Although the scoring of such
interactions remains crude [34] , it is particularly
helpful in such context to prioritize the chemistry effort on the promising fragment derivatives. The strength of this approach can also be
its main limitation, when it is driven primarily by
ease of synthetic chemistry and reagent accessibility, without maximizing opportunities to meet
the structural constraints imposed by the receptor. Thus, the selected synthetic chemistry must
take the targeted site into account even before
docking of the resulting library, in particular
regarding the linkers imposed by the chemistry.
A more general approach would be to use
the principles of de novo design methods [35,36]
to guide elaboration of the fragment hits. This
strategy is not restricted to a preselected chemistry or list of reagents, and computationally generates ideas directly selected to maximize their
structural match to the receptor. Even under the
receptor steric constraints, this approach faces a
combinatorial explosion producing a vast number
of suggestions. The associated chemical diversity and novelty may help, but the large array of
generated ideas must be filtered aggressively on
defined criteria. Pruning with calculated physico­
chemical descriptors relating to ADMET properties is straightforward and routine. However,
reconciling the algorithmically generated ideas
with tractable synthetic chemistry remains a
major bottle neck for the de novo approach. Yet,
starting from an experimentally discovered fragment core means that this key first step does not
have to be tackled computationally. Thus, the
de novo engine can operate directly on a validated fragment, to explore its substituents. So,
Commentary | Foloppe
there is, in principle, a strong complementarity
between FBDD and the de novo design strategy.
Importantly, the de novo tools are very powerful
idea generators. Even if not literally practical, such
ideas can form the basis of fruitful discussions to
inspire medicinal chemistry efforts.
Growing versus linking
Regardless of the precise techniques used to generate and prioritize ideas, there are two avenues
to elaborate fragment hits into leads: growing
and linking [37] . Growing refers to the stepwise
addition of substituents to a fragment anchor, to
target as efficiently as possible the surrounding
binding site. Our experience, and discussions
with other practitioners, indicate that growing
is the most frequent situation, if only because
linking requires that two fragments bind to
adjacent sites on the target. This second situation is, however, sometimes made possible by
the small size of the fragments, and the nature
of the target [4,28,37,38] . Ideally, one should obtain
an x-ray structure with both fragments bound
simultaneously, instead of the fragments crystallized separately, as the binding of one fragment
may influence the other [28] . When presented
with two fragments bound in proximal pockets, the linking approach attempts to find tethers
between them [39] . Examples of linking between
fragments have been reported [4,28,37,38] .
Theoretically, linking has long been recognized as a way to gain binding affinity over that of
each individual constituent fragment, by reducing the penalty arising from the loss in rotational
and translational entropy upon binding [28,40–42] .
Linked fragments can indeed result in more
potent compounds [28,37,38] , even without apparent favorable interactions between the linker and
receptor [38] . Of course, the linker still needs to be
sterically adequate, and selected such that it does
not incur internal strain in its bioactive binding
mode [28,37,38] . Such intramolecular conformational energies can be calculated rather accurately by modern computational chemistry [43] ,
but predicting the other contributions to the free
Rees DC, Congreve M, Murray CW, Carr R.
Fragment-based lead discovery. Nat. Rev.
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energy of binding remains challenging [42] . Yet,
free-energy calculations were reported to have
contributed to some fragment evolutions [11] . The
strong complementarity that exists, in principle,
between FBDD and perturbation-based rigorous
free-energy calculations may become practical in
the future.
Future perspective
Overall, FBDD has established itself as a powerful paradigm for the discovery of medicinal leads
with desirable properties. With this strategy, the
H2L process is arguably as close as one can currently be to rational drug design. It offers realistic
opportunities to obtain leads quickly while controlling their properties. Of course, trial and error
is still part of FBDD, but structure-based design
tools do guide fragment optimization. There are
still ample productivity gains to be realized by
developing more reliable computational design
protocols, integrated with synthetic chemistry.
Another major benefit of FBDD will be to
deepen and sharpen our fundamental understanding of molecular recognition. Indeed, fragment elaboration yields vast amount of systematic
experimental data combining x-ray structures of
protein–ligand complexes and associated binding affinities and kinetics. The mining of such
data to dissect the underlying physical chemistry
of protein–ligand recognition has only begun.
So, documenting well-characterized case studies of fragment elaboration remains invaluable.
One hopes that the lessons learned will go
beyond empiricism and will ultimately inform
the development of more powerful design tools.
Financial & competing interests disclosure
The author is an employee of Vernalis R&D Ltd, a pharmaceutical company that uses fragment-based drug design
as its discovery platform. The author has no other relevant
affiliations or financial involvement with any organization
or entity with a financial interest in or financial conflict
with the subject matter or materials discussed in the
manuscript apart from those disclosed. No writing assistance
was utilized in the production of this manuscript.
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