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Trends in Hit-to-Lead Optimization Following DNA-Encoded Library

Screens
Christopher A. Reiher, David P. Schuman, Nicholas Simmons, and Scott E. Wolkenberg*
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ABSTRACT: DNA-encoded library (DEL) screens have emerged

as a powerful hit-finding tool for a number of biological targets. In
this Innovations article, we review published hit-to-lead opti-
Downloaded via CENTRAL MICHIGAN UNIV on May 14, 2021 at 22:23:42 (UTC).

mization studies following DEL screens. Trends in molecular

property changes from hit to lead are identified, and specific
optimization tactics are exemplified in case studies. Across the studies, physicochemical property and structural changes post-DEL
screening are similar to those which occur during hit-to-lead optimization following high throughputscreens (HTS). However,
unique aspects of DELthe combinatorial synthetic methods which enable DEL synthesis and the linker effects at the DNA
attachment pointimpact the strategies and outcomes of hit-to-lead optimizations.
KEYWORDS: DNA-encoded library, hit-to-lead

T he discovery of hits and their development into tractable

chemical leads is critical to chemical biology and drug
discovery.1 DNA-encoded library (DEL) screens offer the
ability to evaluate million to billion-member compound
libraries within a single experiment at a fraction of the per
compound cost, time, or material burdens of other hit-finding
technologies.2 Each small molecule within a DEL is tagged
with an identifying DNA sequence and, through a multiplexed
selection process, binder or active compounds within the DEL
are identified for follow-up via high-throughput DNA
sequencing. Many variations of this underlying concept have
been developed, numerous examples of successful DEL
syntheses and screens have been reported, and DEL screens
have now become a regular fixture within many organizations’
target hit-finding plans.3,4 Although the frameworks of DEL
synthesis and screening have been reviewed, hit-to-lead Figure 1. Comparison of DNA-encoded library and high-throughput
optimization following DEL screens has received less screening technologies.
attention.5 In this Innovations article, we review recently
published hit-to-lead optimizations following DEL screening,
observe trends, and examine key questions. What are the building blocks. The curation of large, diverse sets of chemical
molecular properties of DEL hits which are selected for hit-to- building blocks with tightly defined physicochemical properties
lead optimization? What strategies are pursued during the can be difficult, leading to product structures that may span
optimization? How different or similar are they to practices outside desirable property ranges. During synthesis, character-
employed optimizing hits from high throughput screens ization is conducted mostly through mass spectrometry, and
(HTS) and other approaches? limited purifications are employedthus, variable yields of

■
expected structures, synthetic truncations,6 undesired side
CHARACTERISTICS OF DEL
DEL exhibits many appealing features and, like any hit-finding Received: November 22, 2020
method, has limitations and artifacts which affect compound Accepted: January 28, 2021
library design, screening, and follow-up. Most DEL chemical Published: February 11, 2021
matter was built through split-and-pool “DNA-recorded”
synthesis using 2−4 cycles of combinatorial DNA-encoded
chemistry, and each cycle may involve dozens to thousands of
© 2021 The Authors. Published by
American Chemical Society https://dx.doi.org/10.1021/acsmedchemlett.0c00615
343 ACS Med. Chem. Lett. 2021, 12, 343−350
ACS Medicinal Chemistry Letters pubs.acs.org/acsmedchemlett Innovations

Figure 2. (A) DEL hits and leads compared to HTS hits, MW plotted versus clogP. Optimizable DEL hits (blue filled circles), leads resulting from
DEL hits (red filled circles), and entire DEL hit space (gray filled circles, ref 12). Janssen historical HTS hit space (purple open circles). (B)
Comparison of the MW between DEL hit and lead pairs. (C) Comparison of the clogP between DEL hit and lead pairs. (D) Comparison of
lipophilic ligand efficiency between DEL hit and lead pairs. (E) Comparison of the ligand efficiency between DEL hit and lead pairs.

reactions, or unidentified byproducts may all be encoded by a
single DNA sequence. Although DEL-compatible reactions are
being continuously developed (e.g., photoredox-based cou-
plings, reversible solid-phase DEL synthesis and C−H
activation), historically DELs made heavy use of a small
number of robust, aqueous reactions (e.g., amidation, sp2
cross-couplings, nucleophilic substitution, and reductive
amination).7 Due to the covalent connection to the associated
DNA tag, individual DEL structures can exhibit linker-based
effects during the screen and hits will often bear functional
groups at the site of linker attachment containing hydrogen
bond donors/acceptors that contribute to hit binding. In
addition, due to the presence of an attached DNA tag, any very
large or highly lipophilic structures formed during DEL
synthesis can be expected to stay solubilized in water during
screening. Within a DEL selection for binders, initial protein−
DEL stoichiometry may be skewed to avoid binding site
competition effectshowever, binder identification is depend-
ent on selection stringency and sequencing coverage,
ultimately leading to preferential identification of higher
affinity compounds.8 This is in contrast to other high-volume
approaches such as HTS in which collections of compounds
are screened as individual, nonlinkered structures prepared
with no inherent limitations on synthetic chemistry or reaction
sequence and with fewer limitations on assay formats or ranges
of compound detection (Figure 1).9,10 A detailed comparison
of screening modalities is beyond the scope of this article, and
readers are referred to ref 3 for an excellent overview.
344
Although design methods to control DEL hit properties have
been proposed,11 complete descriptions of realized DEL
productions and the properties of their enumerated structures
and resulting hits remain scarce. However, several reviews have
surveyed the physicochemical properties of hits arising from
available DEL screen data. A comprehensive 2016 review from
Franzini and Randolph catalogued 155 published DEL hits
across 32 selections.12 In their analysis, the number of
diversification points used in the originating DEL tracked
with increasing hit polar surface area, hydrogen bond donors,
hydrogen bond acceptors, and rotatable bonds. While many
hits contained cLogP values considered within druglike ranges,
the majority of reported DEL hits had molecular weight above
500 Da, and nearly all were above 400 Daproperties
considered to be outside of ideal leadlike space.13,14 Similarly, a
2018 analysis on hits from DEL screens conducted at Roche
revealed hits followed a normal distribution centered around
500 Da.15 Given these reported trends among DEL hits,
several questions arise about the hit-to-lead optimization of
these hits: (1) Do DEL screens, as they have been historically
performed, explore a subset of traditional small molecule
chemical space represented in HTS? (2) Do DEL campaigns
deliver optimizable leads across target classes? (3) Are unique
hit-to-lead tactics applied to DEL-derived hits versus HTS? (4)
What molecular weight and lipophilicity ranges define the
optimizable DEL hit space, and how does this differ from the
total DEL hit space? (5) Is there a greater focus on defining the
minimum pharmacophore, since a linker attachment point is
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ACS Medicinal Chemistry Letters
known; and since truncated sublibraries are present in
screening mixtures?
■ MOLECULAR PROPERTIES OF OPTIMIZABLE DEL
HITS AND CHANGES DURING POST-DEL
HIT-TO-LEAD
To address these questions, we identified peer-reviewed hit-to-
lead optimization studies following DEL screens published
within the past 5 years. Reports which presented compound
data for DEL hits that were limited to on-DNA hit validation,
only explored simple DNA-attachment point hit variants (e.g.,
acid, methyl amide), or only contained very narrow structure−
activity follow-up were excluded from our analysis. After
identifying 15 reports that passed these criteria, for each we
determined structures of the hit and lead.16 Physicochemical
parameters were calculated using a single consistent set of
methods, and hit versus lead property changes were compared.
The list of identified structures, their physicochemical
properties, the target, and the target class are presented in SI
Table 1 (see Supporting Information).
The hits contained in SI Table 1 represent the subset of total
DEL hit space which has been shown to be optimizable. The
hits arise from screens predominantly versus soluble intra-
cellular targets, most commonly enzymes. The DEL library
designs from which the hits originate vary, and just one
example originates from a polypeptide library based on natural
amino acids. The physicochemical properties of this hit and
lead are outliers versus the other structures analyzed.
We compared the MW and cLogP of these optimizable DEL
hits and their resulting leads using a chart based on that in two
prior publications (Figure 2A).6,12 Molecular weight is shown
on the y-axis with 500 Da as a reference line, and clogP is
plotted on the x-axis with reference lines at 1 and 5. DEL hits
are shown as filled circles, with blue denoting hits which were
optimized to leads and gray denoting hits whose optimization
has not been published (gray filled circles are from ref 11).
DEL leads are shown as filled red circles. To add a reference
data set, HTS hits are plotted in Figure 2A as purple open
circles. Because public access to HTS hit structures is limited,
we enabled this comparison using Janssen HTS data, for a
collection of hits published previously.17
Figure 2A compares optimizable DEL hits (blue) and leads
(red) with the total DEL hit space (gray) and Janssen HTS hit
space (purple) across MW and cLogP. The total DEL hit space
lies in a MW range which is higher than the HTS hit space
(∼400−1100 vs ∼200−700 Da), but the cLogP range is
similar. While the overall DEL hit MW range is higher (blue
and gray in Figure 2A), the hits that were demonstrated to be
optimizable (blue) generally fall in a lower MW range (350−
700). This trend is unchanged when the HTS hit data set is
filtered to only those hits which arise from screens versus
enzymes (data not shown) On average, the optimizable DEL
hits had MW 533 and cLogP 3.9, while their leads had MW
552 and cLogP 4.0 (see SI Figure 1).
Molecular weight and clogP changes between pairwise
comparisons of hit and lead (Figures 2B and 2C) revealed
changes in both increasing and decreasing directions and of
variable magnitude. The property changes during DEL hit-to-
lead are consistent with recent analyses of hit-to-candidate
optimizations.4,18,19 In contrast to MW and clogP, ligand
efficiency and lipophilic ligand efficiency parameters showed a
clear and consistent upward trend (Figures 2D and 2E). This
suggests that a variety of tacticstruncation, MW growth, and
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increase or decrease in lipophilicityconsistently resulted in
more potent leads with higher ligand efficiency.
An additional set of trends emerges from examination of
molecular property distributions for HTS hits, all DEL hits,
optimizable DEL hits, and DEL leads (SI Figure 1). Molecular
weight and clogP distributions of all DEL hits span a
significantly broader range than HTS hits, but the distribution
of MW and clogP for optimizable DEL hits does not. The
optimizable DEL hit distributions are narrower and similar to
those for HTS hits. Interestingly, the MW distribution of
optimizable DEL hits is centered at 533, intermediate from the
midpoint of the HTS distribution (410) and total DEL hit
space (631). Unlike MW, the midpoints of the clogP
distributions are more similar (3.6−4.1).
■
EXAMPLES OF HIT-TO-LEAD OPTIMIZATIONS
Changes in molecular properties during hit-to-lead campaigns
based on DEL-derived hits are informative, and a more
detailed examination of specific optimizations reveals what
structural changes underlie the molecular property changes. In
reviewing the published studies, a few trends emerge: (1)
truncation of significant portions of the hit structure; (2) a
focus on reducing lipophilicity; and (3) use of the DNA
attachment vector to introduce polar functionality. These
trends reflect commonly employed tactics in medicinal
chemistryminimum pharmacophore development and mod-
ulation of physicochemical propertieswhich are applied
regardless of hit origin. However, aspects of the DEL hit
optimizations diverge from those of HTS-derived hits, as the
following examples illustrate.
■ ADAMTS-4
Iterative affinity screening of His-tagged ADAMTS-4 (ag-
grecanase-1) using a 4-cycle triazine DEL library provided a
library subfraction which was amplified and sequenced.20 The
sequence enrichment data suggested clear directions for hit
validation and SAR at each of the three triazine substituents as
all chemotypes arising from 4-(aminomethyl)benzoic acid and
a 2,6-disubstituted tetrahydroisoquinoline were highly popu-
lated and no preferred substituent was observed at the
remaining triazine substituent which included the DNA
attachment point (1a−d, Figure 3). This set of observations
represents a rich SAR which emerged directly from the screen.
While a similar data set can sometimes arise following an HTS
for densely populated chemical clusters, regular observation of
SAR trends and hit families has been noted as a common
Figure 3. Hit-to-lead optimization targeting ADAMTS-4.
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ACS Medicinal Chemistry Letters
feature in DEL screens.21 In the case of compounds where
binding affinity has been validated through off-DNA resyn-
thesis and retesting, the SAR observed from DEL sequencing
can qualitatively suggest immediate areas to focus hit
optimization, a clear difference from hit-to-lead following
HTS. In the case of ADAMTS-4, definition of the minimum
pharmacophore was prioritized, and the cycle 1 substituent was
truncated (1a [R = benzylamino] → 1b [R = H], Figure 3)
based on the screening data. An increase in potency was
observed, along with a large decrease in clogP (∼2.5 log units)
and molecular weight (105 Da). Despite the improvement in
molecular properties, polar groups were explored at this same
position to improve solubility. Both anionic and cationic
substituents retained high potency, consistent with the authors’
hypothesis that this vector, the former DNA attachment point,
was exposed to solvent. The use of the DNA attachment vector
to incorporate polar functionality and modulate molecular
properties is a theme which is explored in multiple DEL hit-to-
lead examples.
The solubility-enhancing groups incorporated into
ADAMTS-4 inhibitors significantly increased molecular
weight, and further truncation was explored. In the fully
truncated scaffold (2a, R = H) a ∼100-fold decrease in potency
was observed, and potency could be regained through
reintroduction of a polar group at the DNA attachment vector
(2b, R = dimethylaminoethylamine). The resulting lead
exhibits a balance among potency, lipophilicity, and molecular
weight, and profiling of compounds in this series indicates
selectivity versus other zinc metalloproteinases.
■ IDO1
Hit-to-lead optimization following an IDO1 (indoleamine 2, 3-
dioxygenase 1) DEL screen followed some of the same
trends.22 Selection data suggested no preference at the cycle 1
position within the hit series, and off-DNA resynthesis
validated that truncation at this position and at the DNA
attachment point was tolerated, providing compound 3 with
moderate activity in a peripheral blood mononuclear cell
(PBMC) IDO1 activity assay (Figure 4). Sub micromolar
Figure 4. Hit-to-lead optimization for IDO1.
activity of the validated, truncated hit in a PBMC matrix is
notable and supported further optimization efforts. Replacing
the indole in the screening hit with indazole and separation of
isomers improved potency by >10-fold (4), and the
optimization effort shifted to improvement in pharmacokinetic
properties. Despite the drop in molecular weight and clogP
provided through truncation, 4 exhibited low oral bioavail-
ability and dose escalation led to even lower observed
bioavailability. Compound 4 exhibits low crystalline solubility
in fasted state simulated intestinal fluid (FaSSIF, 18.4 ug/mL),
and the authors hypothesized that improvement in FaSSIF
solubility would boost bioavailability. Despite the knowledge
that a linker for DNA attachment was tolerated at the indazole
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3-position, the authors did not report placement of solubilizing
groups at this vector; rather, a prodrug strategy was pursued
and successfully improved oral bioavailability. Whether
solubilizing groups at the DNA attachment vector would
have led to retained activity or improved solubility is unknown,
and this example illustrates that while a DEL hit always
contains a vector where large polar groups are tolerated, it is
just one of the options medicinal chemists have to optimize
molecular properties.
■ BCATm
DEL screening against mitochondrial branched chain amino-
transferase (BCATm) differed from ADAMTS-4 and IDO1 in
that selection data gave no clear direction for removal of an
entire building block subunit of the structure.23,24 Off-DNA
resynthesis was performed with a methyl amide at the DNA
attachment vector (5), which is commonly used to truncate
the linker region. Enzyme inhibition activity was validated, and
improvement in mouse pharmacokinetic properties was
pursued to enable an in vivo proof-of-concept study.
Replacement of the methylthiophenyl substituent with
pyridine and other heterocycles enhanced potency while
decreasing lipophilicity and molecular weight, and cellular
activity was retained (6a, Figure 5). Truncation of the entire
Figure 5. Top: hit-to-lead optimization for BCATm. Bottom: X-ray
crystal structure of 6a bound to BCATm; the DNA attachment vector
is indicated in the yellow box. (PDB code 5HNE).
methyl amide substituent led to a loss of potency (6b), and
small modifications including dimethyl amide (6c) were not
tolerated, suggesting the DNA attachment vector was sensitive
to structural modification. Insight into the potency SAR at this
position was provided by an X-ray cocrystal structure of 6a in
complex with BCATm. At the DNA attachment vector, the
methyl amide makes separate H-bond donor and acceptor
interactions, and the methyl group is oriented toward a small
hydrophobic pocket, consistent with the SAR that larger
substituents are not tolerated. The amide N−H bond is
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oriented toward solvent, suggesting that during the DEL screen provides additional evidence for the utility of exploring polar
the linker and DNA are accommodated with this trajectory. substituents at the DNA attachment vector; just as important,
The X-ray structure corroborated the SAR that cis stereo- however, it shows that modulation of molecular properties was
chemistry was preferred within the 1,3-diaminocyclohexyl unit. achieved through exploration of changes throughout the entire
A takeaway from this study is that while the DNA attachment structure and not only at the DNA attachment point (Figure
vector of a DEL-derived hit must by definition accommodate a 6).
large hydrophilic substituent, off-DNA hit optimization should
also explore nonpolar substituents at this position. It is not
assured that property modulation via polar substituents at this
vector will be tolerated or beneficial.25 In the end, property
modulation via incorporation of pyridine at the benzimidazole
2-position provided improvements in mouse pharmacokinetic
properties sufficient to enable successful measurement of
BCATm inhibition in vivo following oral dosing.

■ BRD4
In a separate study, DEL screening identified a structurally
novel second generation bromodomain and extraterminal
(BET) inhibitor using His-tagged BRD4.26 The hit-to-lead
optimization strategy was derived from an analysis of attrition
causes for the first generation BET inhibitors as well as the risk
of submaximal target engagement for these compounds due to
low systemic concentrations following oral dosing. The
strategy therefore emphasized physicochemical properties,
solubility, and predicted human daily dose. As with
ADAMTS-4 and IDO1, sequencing data on the enriched
library fraction following affinity screening immediately
indicated that cycle 3 building blocks contributed little to
binding. Once again, truncation was explored at the off-DNA
resynthesis and hit validation stage, and the piperidine N-
acetamide analog of 7 was selected as the starting point for
optimization due to its favorable hit profile, in particular
ChromLogD7.4,27 PFI (Property Forecast Index),28,29 LE,30 Figure 6. Top: hit-to-lead optimization for BRD4. Bottom: X-ray
and LLE.30 Notably, hit-to-lead progressed with deletion of the crystal structure of 8 bound to the first bromodomain of BRD4; The
methyl amide at the benzimidazole 6-position, the DNA DNA attachment vector is indicated in the yellow box. (PDB code
6TPZ.)
attachment vector, as this gave a further improvement in PFI.

As a result of the extensive truncations, the starting point for
off-DNA optimization had a molecular weight of 377, whereas
the on-DNA structures detected in the DEL screen had
molecular weights >500 Da. Replacement of the 2,6-
dimethylphenol was prioritized to improve mouse pharmaco-
kinetic properties, and a pyridinone isostere retained potency
and improved PFI, LE, and LLE substantially. Incorporation of
the pyridinone was suggested by the X-ray structure of a
structurally related fragment bound to BRD4; the fragment
originated from a screen unrelated to the DEL screen. The
property-enhancing pyridinone was combined with further
truncation of the piperidine to provide pyran 7a which, despite
its low molecular weight, high solubility, and desirable
physicochemical properties, had a predicted human dose
outside the acceptable range. Potency enhancement, further
improvements in pharmacokinetics, and maintenance of high
solubility became the focus. While the dimethoxypropyl analog
of pyran 7b was improved across these parameters, dose
projections remained high. Therefore, the authors pursued
substituents at the benzimidazole C5 and C6 positions.
Incorporation of a polar substituent at C5 was suggested
both because this was the DNA attachment vector and
because, unsurprisingly, X-ray crystal structures indicated this
position is oriented toward solvent. A number of N-linked
amines were investigated and morpholine 8 provided sufficient
improvement in both potency and metabolic stability to
generate a >100× lower human dose prediction. This study
347
■
DDR1
Discoidin domain receptor 1 (DDR1) and its homologue
DDR2 were subjected to DEL screening of pooled chemical
libraries using a range of protein concentrations in an iterative
protocol.31 A spirocyclic imidazolinone hit was prioritized
based on selectivity for DDR1 over DDR2 and structural
novelty among reported receptor tyrosine kinase inhibitors.
Sequencing data from the screen did not support truncation of
any building block units, and improvements in potency,
solubility, and microsomal stability were pursued based on
validated hit 9a, which contains a methyl amide at the DNA
attachment vector (Figure 7). An X-ray cocrystal structure of
DDR1-bound 9a indicated that this amide bound near an
unoccupied hydrophobic pocket, and analogs which extend the
methyl amide, such as the trifluoroethyl amide, improved
potency ∼100×. As described above in the case of BCATm,
the placement of a lipophilic substituent at the DNA
attachment vector can be counterintuitive, since this vector
by definition accommodates a large polar substituent. The
DDR1 structure, however, demonstrates that an unoccupied
lipophilic pocket can be found in proximity to solvent-exposed
surfaces of the protein. Additional DDR1 SAR supports this
observation, since morpholinoethyl amide 9c, which projects a
polar substituent at the same position, boosts potency and
decreases lipophilicity. A combination design exploring
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ACS Medicinal Chemistry Letters
Figure 7. Top: hit-to-lead optimization for DDR1. Bottom: X-ray
crystal structure of 9a bound to DDR1; the DNA attachment vector is
indicated in the yellow box. (PDB code 6FEW.)
simultaneous occupancy of the lipophilic pocket as well as
projection of a polar group toward solvent was successful, and
N-hydroxyethyl, N-trifluoroethyl amide 9d maintained high
potency and reasonable measured logD while increasing
aqueous solubility >10-fold. This is a unique example of the
DNA attachment vector being leveraged for both hydrophobic
interactions and polar substitutions within the same com-
pound. However, the property improvements came with a
substantial increase in molecular weight, and human and
mouse metabolic stability were poor versus the DEL hit
(compare 9d and 9a). As in the BET hit-to-lead example, the
authors explored reducing lipophilicity not only by leveraging
the DNA attachment vector but also by incorporating polarity
throughout the structure; in this case indazole → azaindazole
substitution (10) provided the same potency, logD, and
solubility improvements with a significantly lower molecular
weight and improved metabolic stability. The resulting lead
was further optimized to provide a tool suitable for in vivo
proof-of-concept studies.
■
SUMMARY
We identified and analyzed recent published accounts of hit-to-
lead optimization following DEL screens. A number of trends
in molecular property changes and specific medicinal chemistry
tactics were observed. Although in many respects the trends
observed here are consistent with hit-to-lead approaches
following HTS, there were also notable differences.
The nature of hit optimization is heavily influenced by the
goals of the program and the properties of the hitmost
studies we analyzed sought orally bioavailable leads; thus, the
target property range was consistent with the well-described
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space of orally bioavailable small molecule drugs.18 The
properties of DEL-derived hits, however, were significantly
different from HTS-derived hits. A portion of DEL hits
overlaps with HTS hit space (clogP vs molecular weight), but
as a group DEL hits were higher molecular weight than HTS
hits (see Figure 2A). This finding is consistent with the split-
and-pool, molecular weight additive synthetic routes com-
monly employed in DEL synthesis. Notably, DEL hits and
HTS hits span a similar distribution of clogPa consequence
of the wide array of polar and nonpolar building blocks that
may be utilized in DEL builds largely unencumbered by
difficult substrate-specific purifications.
Although DEL hit space partially overlapped with HTS hit
space, the majority of DEL hits selected for optimization lay
within the HTS hit space. This trend may result from selection
bias, where lower molecular weight DEL hits are favored, or
publication bias; in either case optimizable DEL hits arose
disproportionately from this lower molecular weight range. In
addition, the clogP of DEL hits selected for optimization lies
within a narrower range than the overall DEL or HTS hit clogP
range (∼1 to 6 versus −2 to 8, Figure 2A and SI Figure 1). Hit-
to-lead optimizations of DEL hits emphasize truncations and
identification of the minimum pharmacophore. This is a
universal optimization strategy; however, it also aligns with the
need for molecular weight reduction to achieve oral
bioavailability from a high molecular weight DEL hit. Ligand
efficiency emerged as the single parameter which universally
increased during optimization, and lipophilic ligand efficiency
had a strong increasing trend as welldespite variable changes
in molecular weight and clogP across the studies. The LE and
LLE changes appear to reflect the focus on truncation, potency
enhancement, and an additional major trend, reducing
lipophilicity. While optimizing the balance among potency,
lipophilicity, and molecular weight is not unique to DEL
derived chemical matter, aspects of how this was pursued in
the DEL hit-to-lead studies reflected special considerations
present in DEL. Lastly, the degree of structural modification
from hit to lead varied and was, in some cases, considerable, as
Tanimoto similarity between hits and leads ranged from 0.6 to
0.96. This is consistent with some optimizations introducing
substantial core modification and not only varying substituents
around a consistent scaffold.
Given the trends we observed, what should medicinal
chemists consider when optimizing hits from DEL screens? (1)
Leverage the SAR available from screening whenever possible
and in particular to define the minimum pharmacophore. (2)
Exploring the SAR of the DNA attachment point is productive
and should include truncation, simple amides (primary,
methyl, and dimethyl), and polar, nonpolar, and amphiphilic
substituents. Consider acyclic tertiary amides simultaneously
projecting a nonpolar and a polar group away from the
scaffold. (3) The DNA vector may be oriented toward solvent
and provide a handle to optimize physicochemical properties,
but it is possible and worth considering that the DNA vector
may point to a hydrophobic pocket which can be exploited for
potency gains. (4) Leverage X-ray cocrystal and other
structural information to inform designs at the DNA vector
and throughout the structure. (5) If the goals of the
optimization include oral dosing, pursue lower MW hits even
if less potent.
A limitation of our analysis is that the protein targets in
published DEL hit-to-lead studies represent only a narrow
subset of target space being pursued in drug discovery.21
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Enzymes are far overrepresented (13 out of 15 DEL hit-to-lead
papers, versus 28% of drugs32) and DEL hit-to-lead success
rates and trends may differ for nonenzyme targets. Interest-
ingly, DEL screens for other target classes have been
reported,33−35 both for soluble (including nuclear receptors,
structural proteins, and transcription factors) and membrane-
bound proteins (GPCRs). But hit-to-lead optimizations based
on these screens have not been published; it is unclear from
the literature whether this reflects the optimizability of DEL
hits for these targets. Targeted protein degradation is an
emerging area with high potential for DEL impact, but studies
describing evolution of DEL screening hits to degraders have
not yet appeared. The outcome of hit-to-degrader optimiza-
tions, which lie in the beyond-rule-of-five property space, will
likely differ from those in the traditional small molecule space.
As further refinements in DEL design strategy and newer
DEL chemistries make their mark within DEL screening
collections, the properties of DEL hits will evolve and so will
hit-to-lead optimizations. Novel DEL-compatible reactions
may shift DELs toward more targeted, smaller-sized 2- or 3-
cycle libraries that are within a more traditional HTS chemical
hit space. Furthermore, new advancements in the analysis of
DEL selection data may allow better understanding of lower-
enriched structure−activity relationships36 or train predictive
models34 to enable prioritization of hits that have improved
physicochemical properties. Continued innovation in DEL
design and synthesis is likely, and the hits which emerge from
novel libraries will continue to drive hit-to-lead and the
invention of future clinical candidates and drugs.
■
ASSOCIATED CONTENT
*
sı Supporting Information
The Supporting Information is available free of charge at
https://pubs.acs.org/doi/10.1021/acsmedchemlett.0c00615.
Literature search strategy; method of analyzing papers;
characteristics of hit-to-lead studies; molecular property
distributions for DEL hits, DEL leads, and HTS hits;
DEL hit and lead structures and physicochemical
properties (PDF)
■
AUTHOR INFORMATION
Corresponding Author
Scott E. Wolkenberg − Discovery Chemistry, Janssen Research
& Development, LLC, Spring House, Pennsylvania 19477,
United States; orcid.org/0000-0003-0840-6593;
Email: swolkenb@its.jnj.com
Authors
Christopher A. Reiher − Discovery Chemistry, Janssen
Research & Development, LLC, Spring House, Pennsylvania
19477, United States; orcid.org/0000-0002-6171-3480
David P. Schuman − Discovery Chemistry, Janssen Research
& Development, LLC, San Diego, California 92121, United
States
Nicholas Simmons − Discovery Chemistry, Janssen Research
& Development, LLC, San Diego, California 92121, United
States; orcid.org/0000-0003-0766-5382
Complete contact information is available at:
https://pubs.acs.org/10.1021/acsmedchemlett.0c00615
349
pubs.acs.org/acsmedchemlett Innovations
Author Contributions
The manuscript was written through contributions of all
authors.
Notes
The authors declare no competing financial interest.
■
ACKNOWLEDGMENTS
We thank Michael D. Hack and Arjun Saha for summary data
describing Janssen HTS screen hits and Zhicai Shi for critical
feedback on the manuscript.
■
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