Communications
From the enumerated library, we immediately excluded com-
pounds that were clashing with the receptor and we focused
on compounds that had the right size and orientation to bind
to the active site. Although, very weak binders, such as
compound 3b could not be excluded at this stage of the Experimental Section
docking selection, they still provide interesting structural
information for further optimization of the scaffold. It should be
noted that accurate correlating of the binding poses with the
biological activity is not possible and is beyond the aim of the
developed workflow. However, this anchor-based approach Acknowledgements
shows how an anchor warhead can be incorporated in an MCR
resources and in shorter times compared to strategies that still
involve a significant serendipity and random trial component.
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scaffold and be optimized without major synthetic effort.
In summary, we introduced a generalized protocol for the
AnchorQuery approach which overcomes current limitations of
amino-acidogenic anchors. Anchors are significantly affinity
contributing fragments in protein binding and more general in
receptor-ligand interactions. Thus, anchor fragments comprise
valid starting points for growing leads that can be validated
rapidly if combined with a high diversity convergent chemistry,
such as MCR.
Thus, we designed an MCR scaffold with a novel warhead
for aspartic proteases. In this approach, the scaffold could be
accessed with a simple two-step methodology. The biological
evaluation of the hits together with the determined crystal
structures, indicate that the design and optimization of our
libraries was successful. Although these are yet not highly
potent inhibitors for this enzyme, we were able to analyze the
interactions of our MCR scaffold and gained valuable insights
regarding the adopted binding modes.
This research was supported (A.D., G.K., and J.C.C.) through ITN
“Accelerated Early stage drug dIScovery” (AEGIS, grant agreement
no. 675555). Moreover, funding was received from the US National
Institutes of Health (NIH, grant 2R01GM097082-05), the European
Lead Factory (IMI) (grant agreement no. 115489), the Qatar
National Research Foundation (NPRP6-065-3-012), COFUNDs
ALERT (grant agreement no. 665250), Prominent (grant agreement
no. 754425), and KWF Kankerbestrijding grant (grant agreement
no. 10504). Funding from the Helmholtz Association’s Initiative
and Networking Fund, COFUNDs ALERT (grant agreement No
665250) and the European Research Council (ERC starting grant
757913) is gratefully acknowledged (A.K.H.H.). Authors F.M., A.H.,
and G.K. thank the MX-team at BESSY II (Helmholtz-Zentrum
Berlin, Germany) for their advice during data collection and
particularly acknowledge the help and support of Dr. Manfred
Weiss, Dr. Christian Feiler, Dr. Franziska Huschmann, and Dr. Jan
Wollenhaupt. They also thank the Helmholtz-Zentrum Berlin for
travel support.
Moreover, the docking protocol for tailor-made virtual
libraries can be applied to different chemical reactions and
fragments, enabling computational evolution of libraries that Conflict of Interest
are not part of public databases. The choice of the fragment-
anchor is the determining step in this protocol and should
include a sequence of atoms that are present as a common
motif throughout the entire library. These atoms should
significantly contribute to the binding interactions between the
designed ligands and the protein. For instance, the anchor
could be the motif binding in the enzyme’s active site, whereas
in protein-protein interactions, it could be a moiety deeply
buried in the interface.
To the best of our knowledge, currently available docking
software cannot optimize a specific scaffold/chemistry of
interest by focusing on the possible combinations of commer-
cially available starting materials. The libraries in this approach
are not limited to multi-component reaction (MCR) scaffolds
only but any sequence of organic reactions would work
similarly. Broader chemistry schemes can be applied, including
post-modifications. We envision future applications either for
docking of novel scaffolds towards biological targets or for
optimizing a scaffold of interest. As shown in this case study,
departing from commercially available starting materials,
thousands of compounds could potentially be accessed. Our
protocol can significantly support the decision-making process
of prioritizing docking hits as subsequent candidates for
chemical synthesis and will lead to the requirement of fewer
The authors declare no conflict of interest.
Keywords: hydrazine-tetrazoles · MCR chemistry · docking
protocol · aspartic protease · crystal structures
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