CASE STUDY

Design of a highly
selective, allosteric,picomolar TYK2
inhibitor using novel
FEP+ strategies
Computationally-guided, structure-based drug design strategy drives
discovery of potentially best-in-class TYK2 inhibitor

First application of large-scale
free energy perturbation (FEP+)
in drug discovery

Extensive use of a novel
physics-based method topredict solubility“

Our teams designed, iterated,and optimized leads using
next-generation, physicsbased technologies, whichallowed us to rapidly refine
our discovery methodologies.
This partnership providedNimbus with unparalleledcomputational horsepower
and unprecedented FEP+
modeling efforts.”— Craig Masse
Former Head of Medicinal Chemistry, Nimbus Therapeutics

First discovery of novel
picomolar cores with FEP+

TargetTYK2 kinase

ProgramType

Collaborative program,small moleculePartner

Nimbus Therapeutics

Indication

Inflammatory diseases,
psoriasis

StagePhase 2b → Phase 3
clinical trial

DESIGN CHALLENGE
JAK/TYK kinases are key signaling molecules
in a variety of inflammatory diseases. In
psoriasis, for example, inflammation isdriven by increased interferon and cytokine
release, which is regulated by these JAK/TYK kinases. To date, marketed drugs havetargeted the JH1 kinase domain of these
multi-domain protein complexes. However,these approved JAK inhibitor drugs have
known safety issues related to heart
function, clotting, and thrombosis due tonon-selective inhibition of other JAK kinases(JAK1, JAK2, JAK3).
Scientists from Nimbus Therapeutics began
working on this challenge with the goal ofdeveloping a potent and highly selectiveTYK2 inhibitor that improved clinical activity
while avoiding off-target side effects. In
2016, Nimbus and Schrödinger scientists
teamed up on the project, first starting bytargeting the catalytic JH1 kinase domain
and later pivoting to the regulatory domain
JH2 based on the release of promising datain the literature.

Enumeration &Hand-Drawn Ideas

4000

Targeting the TYK2 JH1 catalytic
domain: Breakthroughs inTYK2 selectivity and solubility
using large-scale FEP+The high sequence similarity of TYK2 within the JAK family poseda significant selectivity challenge — the TYK2, JAK1, JAK2, and JAK3
ligand binding sites are practically identical. To design a highly
selective and potent molecule that maintains activity while avoiding
off-target liabilities, the team used large-scale, physics-based
simulations to differentiate the binding between the kinases. First,
free energy perturbation calculations using FEP+ were used to
predict the potency on-target on TYK2, as well as to predict thepotency off-target on JAK2 and JAK3.1 Next, the team introduced
a novel approach for predicting aqueous solubility using absolute
FEP+ in order to address ADME properties during modeling.2
With these modeling approaches in hand, the next turning pointin the program was the development of a large-scale FEP+ scoring
campaign to tackle this multiparameter optimization (MPO)
challenge. The team leveraged extensive medicinal chemistry
and modeling expertise to enumerate 4,000 high-quality idea
molecules, all of which had passed preliminary triage through
MM-GBSA and physical property filters.3 Then FEP+ was used
to score the potency, selectivity, and solubility of the molecules(Figure 1). Accomplishing this large scale application of FEP+
scoring required deploying FEP+ to cloud computing resources
at scale, which since this initial effort has become a commonlyused approach. Ultimately, 46 molecules were prioritized on
the basis of the FEP+ calculations for synthesis, and 9 of thesemolecules were found to meet potency, selectivity, and solubility
criteria of the project in later experimental testing. This resulted
in a development candidate targeting the TYK2 JH1 domain thatwas highly selective against JAK2 and moderately selective against
JAK1 and JAK3.

Pyridino-imidazolemolecules

FEP+De NovoCoreDesignVirtualScreening

On Target TYK2:
Potency FEP+

Pyrazolo-pyrimidine

Thiophene-pyrimidine

Oﬀ Target JAK2/3:
Selectivity FEP+

Pyrrazolono-pyridine

Multiple TYK2 JH2crystal structures

Solubility FEP+
Synthesis

46

molecules

9

Pyrazolo-pyrimidinone
Conﬁrmed picomolar
scaﬀolds within 3 months

molecules
were found to meet the potency, selectivity,and solubility project criteria

Figure 1: FEP+ approach used to design
TYK2 inhibitor targeting JH1 domain which
addressed the MPO challenges.

Figure 2: FEP+ de novo core design and virtual
screening strategies employed to identify novel hitstargeted to the TYK2 JH2 domain.

2Pivot to TYK2 JH2 allosteric domain enabled by FEP+ de novo core
design and virtual screening
Around the same time, new research from scientists
at Bristol Myers Squibb confirmed that highly selective
TYK2 inhibitors could be achieved by targeting the JH2
allosteric site.4 The project team made the important
decision to pivot — changing their focus to developing
a TYK2 inhibitor targeting the JH2 regulatory domain.
This biological validation along with the deep structural
enablement available for TYK2 and the JAK family
member pseudokinase domains provided the team with
an opportunity to engage in a multi-pronged, structurebased design strategy.
FEP+ was used to guide compound design strategies withde novo core exploration resulting in the identificationof the pyrrazolono-pyridine and pyridino-imidazole
cores, which displayed promising potency and domain
selectivity but were hindered by several ADME liabilities(Figure 2).5 A large-scale structure-based virtual screen
enabled screening of 2.4M commercially availablecompounds against an ensemble of receptor models
based on known JH2 crystal structures from the PDB
using Glide followed by WScore — resulting in threestructurally distinct hit classes (Figure 2).5 Each hit
displayed some promising level of JH2 affinity, but
the pyrazolo-pyrimidine core was chosen for further
exploration based on its steric and electronic similarity
to the imidazopyridazine core published by BMS. These
structure-based design efforts allowed the team to
identify multiple picomolar JH2 scaffolds from these hits
in a period of 3 months.

properties, as well as passive permeability, wasperformed to ensure the compounds progressed toresource intensive FEP+ models and synthesis would
stay in a reasonable chemical space. Second, compounds
were put through rigorous FEP+ potency predictions— targeting picomolar potency. All models and MPOs
were collected in LiveDesign, Schrödinger’s cloudbased enterprise informatics platform, within different
LiveReports for different design objectives which theteam would review together. Using this MPO strategy,
the team carried out parallel ligand FEP+ modelingagainst TYK2 JH2 as well as other JAK family kinasedomains in order to design analogs with high JH2 affinity
and JAK family domain selectivity.
Within two years of pivoting to the allosteric TYK2
program, the team had declared a development
candidate. NDI-034858 is a picomolar inhibitor tuned
precisely to target the JH2 domain of TYK2, as shown by
its exquisitely clean selectivity profile (Figure 3).
In November 2022, Nimbus reported positive topline
results for once-daily, oral dosing with NDI-034858 inPhase 2b clinical trials.6 Furthermore, by February 2023
Takeda had acquired the program.7 Now referred to as
TAK-279, this highly selective, oral TKY2 inhibitor has
best-in-class potential among allosteric inhibitors fortreatment of psoriasis, as well as multiple other immunemediated diseases.8

In order to progress these hits, the team again employed
an MPO paradigm with large scale modeling, this timein two stages. First, quick modeling of physicochemical

NDI-034858(TAK-279)

In Vitro Potency / Selectivity

NDI-034858 (TAK-279)

TYK2 JH2 Kd

0.0038 nM

TYK2 PBMC IL-12 pSTAT4 IC50

8.4 nM*hWB IFNα IP-10 IC5051 NM*

mWB IFNα IP-10 IC50347 NM*

rWB IFNα IP-10 IC50
JAK1-3 JH1 / TYK2 JH1 Kds

91 nM>30,000 nM

JAK1 JH2 Kd

5,000 nM

JAK2 JH2 Kd

23,000 nM

JAK2 PBMC GM-CSF pSTAT5 IC50>50,000 nM*

JAK1/3 PBMC IL-2 pSTAT5 IC50>50,000 nM*

PDE4D IC50>10,000 nM*

hERG (Patch Clamp) IC50

>30,000 nM*

87 target panel of enzymes, ionchannels, receptors @ 10,000 nM<50% inh for 85 targets*** Geometric means, n≥ 3** Targets with >50% inhibition: LCK (54%i), adenosine transporter (53%i)

Figure 3: NDI-034858 (TAK-279) in vitro potency and off-target selectivity.

3

Enabling digital technologies to drive discovery programs
FEP+Glide

WScoreLiveDesign

High-performance freeenergy calculations forlarge-scale predictionof potency, selectivity,and solubility

Highly versatile, industryleading ligand-receptor
docking solution

Advanced docking andscoring solution poweredby water network analysis

Collaborative enterprise
informatics platform
for centralizing accessto virtual and wet lab
project data and powerfulcomputational predictions

Software and services to meet your organization’s needs
Industry-Leading Software Platform
Deploy digital drug discovery workflows using a comprehensive and user-friendly platform for molecularmodeling, design, and collaboration.

Modeling Services
Leverage Schrödinger’s team of expert computational scientists to advance your projects through key stages
in the drug discovery process.

Scientific and Technical Support
Access expert support, educational materials, and training resources designed for both novice andexperienced users.

References
1.

Advancing drug discovery through enhanced free energy calculations. Abel et al. Acc. Chem. Res. 2017, 50, 7, 1625–1632.

2.

Potent and selective TYK2-JH1 inhibitors highly efficacious in rodent model of psoriasis. Leit et al. Bioorg. Med. Chem. Lett.
2022 Oct 1, 73,128891.

3.

Accelerating drug discovery through tight integration of expert molecular design and predictive scoring. Abel et al.
Curr. Opin. Struct. Biol. 2017 Apr, 43, 38-44.

4.

Tyrosine kinase 2-mediated signal transduction in T lymphocytes Is blocked by pharmacological stabilization of its
pseudokinase domain. Tokarski et al. J Biol Chem. 2015 Apr 24, 290(17), 11061-74; Identification of imidazo[1,2-b]pyridazine
TYK2 pseudokinase ligands as potent and selective allosteric inhibitors of TYK2 signalling. Moslin et al. MedChemComm.
2016 Dec 15, 8(4), 700-712.

5.

Discovery of a potent and selective tyrosine kinase 2 inhibitor: TAK-279. Leit et al. J. Med. Chem. 2023, 66, 15, 10473–10496.

6.

Nimbus Therapeutics announces positive topline results for phase 2b clinical trial of allosteric TYK2 inhibitor in psoriasis.
Nimbus Therapeutics. 2022.

7.

Takeda completes acquisition of Nimbus Therapeutics’ TYK2 program subsidiary. Takeda. 2023.

8.

Takeda announces positive results in phase 2b study of investigational TAK-279, an oral, once-daily TYK2 inhibitor, in people
with moderate-to-severe plaque psoriasis. Takeda. 2023.

Contact us: sales@schrodinger.com
Learn more: www.schrodinger.com/platform

Copyright © 2024 Schrödinger, Inc.

4