Small molecules can self-assemble
in aqueous solution into a wide
range of nanoentity types and sizes (dimers, n-mers,
micelles, colloids, etc.), each having their own unique properties.
This has important consequences in the context of drug discovery including
issues related to nonspecific binding, off-target effects, and false
positives and negatives. Here, we demonstrate the use of the spin–spin
relaxation Carr–Purcell–Meiboom–Gill NMR experiment,
which is sensitive to molecular tumbling rates and can expose larger
aggregate species that have slower rotational correlations. The strategy
easily distinguishes lone-tumbling molecules versus nanoentities of
various sizes. The technique is highly sensitive to chemical exchange
between single-molecule and aggregate states and can therefore be
used as a reporter when direct measurement of aggregates is not possible
by NMR. Interestingly, we found differences in solution behavior for
compounds within structurally related series, demonstrating structure–nanoentity
relationships. This practical experiment is a valuable tool to support
drug discovery efforts.
A rapid and practical approach for the discovery of new chemical matter for targeting pathogens and diseases is described. Fragment-based phenotypic lead discovery (FPLD) combines aspects of traditional fragment-based lead discovery (FBLD), which involves the screening of small-molecule fragment libraries to target specific proteins, with phenotypic lead discovery (PLD), which typically involves the screening of drug-like compounds in cell-based assays. To enable FPLD, a diverse library of fragments was first designed, assembled, and curated. This library of soluble, low-molecular-weight compounds was then pooled to expedite screening. Axenic cultures of Leishmania promastigotes were screened, and single hits were then tested for leishmanicidal activity against intracellular amastigote forms in infected murine bone-marrow-derived macrophages without evidence of toxicity toward mammalian cells. These studies demonstrate that FPLD can be a rapid and effective means to discover hits that can serve as leads for further medicinal chemistry purposes or as tool compounds for identifying known or novel targets.
Fragment-based
lead discovery has emerged over the last decades
as one of the most powerful techniques for identifying starting chemical
matter to target specific proteins or nucleic acids in vitro. However, the use of such low-molecular-weight fragment molecules
in cell-based phenotypic assays has been historically avoided because
of concerns that bioassays would be insufficiently sensitive to detect
the limited potency expected for such small molecules and that the
high concentrations required would likely implicate undesirable artifacts.
Herein, we applied phenotype cell-based screens using a curated fragment
library to identify inhibitors against a range of pathogens including Leishmania, Plasmodium falciparum, Neisseria, Mycobacterium, and flaviviruses.
This proof-of-concept shows that fragment-based phenotypic lead discovery
(FPLD) can serve as a promising complementary approach for tackling
infectious diseases and other drug-discovery programs.
Dengue virus (DENV) is a
Flavivirus
that causes the most prevalent arthropod-borne viral disease. Clinical manifestation of DENV infection ranges from asymptomatic to severe symptoms that can lead to death.
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