Structural Chemogenomics Group

Laboratoire d'Innovation Therapeutique, UMR7200 CNRS/Universite de Strasbourg

Our team aims at rationalizing and accelerating the discovery of innovative bioactive molecules. It stands at the interface of many disciplines (informatics, medicinal chemistry, structural biology, pharmacology) and therefore attracts students from quite diverse areas of expertise. We do perform virtual screening and medicinal chemistry optimization in-house along three main research areas:

· Virtual Screening

· Hit optimization

· Unravelling molecular mechanisms of action

Virtual Screening

Our team has has played a pioneering role in promoting virtual screening in Europe (Bissantz et al. 2000) and keeps on developing and applying in silico screening methods.

1. Databases

· Bioinfo-DB: repertoire of 9 million commercially available drug-like compounds from >25 suppliers (see more )

· sc-PDB: archive of 10 000 druggable-protein ligand complexes, used worldwide for structure-based drug design (> 220 citations; see more )

2. Methodological developments

· ChemoGen: virtual screening in cgemogenomics space with in-house devloped kernels (see more)

· Grim: description of protein-ligand interaction patterns by graphs (see more), recently ranked 2^nd/43 for predicting binding poses in the D3R Grand Challenge 2015 (see more)

· Profiler: off-target prediction method, using a mix of ligand-based (2D and 3D similarity search, pharmacophore search) and structure-based docking approaches (see more)

· RLPharm: automated method to define protein-ligand based pharmacophores, developed in collaboration with BIOVIA (see more). Has led to a unique collection of > 140K pharmacophores for studying either off-target activity or for drug repurposing (see more)

· VolSite: automated detection of protein cavities and druggability estimate (see more)

3. Recent in silico screening applications

We have undertaken 14 in silico screen campaigns over the last 5 years, mostly with the objective to identify the very first ligands of novel targets of high pharmacological value.

Target	Method	Query	Screened	Tested	Hits	Reference
TrkB	Docking	Inhibitors	78045	22	2 @10 µM	Cazorla et al. 2011
TrkB	Pharm^a	PAM^b	8 061	45	2 @10 µM	Not published
OXYR	FPLP^c	Antagonists	336678	120	10 @10µM	Weill et al., 2011
GLR	Docking	NAM^d	7378	22	3 @10 µM	de Graaf et al., 2011
PrP^sc	Docking	Inhibiteurs	350000	32	1 @20 µM	Ayrolles-Torro et al., 2011
Stat3	Docking	Inhibiteurs	78119	9	1 @50µM	Pudlo et al., 2015
*SmNACE*	Docking	Inhibiteurs	61166	98	20 @100µM	Jacques et al., 2015
FLT3	Docking Pharm	Inhibiteurs extracellulaires	343847	60	6 @100µM	WO 2016016370 A1
Lingo-1	Docking	PPI^e	174327	145	3 @20µM	Not published
Integrin α5β1	Pharm+ Docking	NAM	6247	67	3 @50µM	Not published
CD38	Docking Pharm	Inhibiteurs	254713	177	67 @100µM	Not published
Mfd	Docking	Inhibiteurs		95	4 @50µM	Not published
Smoothened	Docking + Pharm	NAM	1300000	67	6 @5µM	Not published

^{^aPharmacophoric search, ^bpositive allosteric regulator, ^cchemogenomic screening, ^d negative allosteric
regulator, ^eprotein-protein interface stabilisers}

Altogether, we have identified 42 hits which were fully confirmed experimentally and led to medicinal chemistry hit to lead optimization programs (TrKB, Stat3, SmNACE, CD38, FLT3, intéine a5b1, Mfd, Smoothened). Among the most interesting hits, we have notably found:

· the very first nanomolar extracellular inhibitor of the TrkB tyrosine kinase receptor (ANA-12) with potent in vivo antidepressant and anxiolytic properties;

· the first TrkB positive allosteric modulator (TB001), inducing a TrkB specific neurite growth with potential applications in neurodegenerative diseases;

· the first extracellular inhibitor of the FLT3 tyrosine kinase receptor (BDT001) with potent anti-hyperalgesic properties in rodent models of neuropathic pain;

· inhibitors of the Smoothened oncogene, targeting the homodimeric form of the receptor, with potent anti-tumoral activities

· inhibitors of the Mfd virulence factor, with antibacterial properties in multi drug resistant infections.

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Medicinal Chemistry Optimization of

In Silico Hits

Pharmacodynamic and pharmacokinetic properties of our in silico hits are optimized in-house by our medicinal chemistry group. Here are 3 examples:

1. TrkB extracellular inhibitors

Trkb is the tyrosine kinase receptor for BDNF (Brain derived neurotrophic factor), a potent neurotrophin essential for neuronal growth. Our Trkb extracellular inhibitor (ANA-12) is potent (IC₅₀ = 4.3 nM), selective (vs. Trka1 and TrkC) and exhibits potent antidepressant and anxiolytic properties in rodents when administered i.p. at the dose of 0.5 mg/kg. Within the framework of an ANR grant (TrkBDNFarmod: ANR 11-BSV4-017-02, we have synthesized 57 analogs by varying the heteroaromatic ring A, the three amide bonds, the core aromatic ring B and the lactame C.


ANA-12 bound to TrkB	Chemical variations on TrkB antagonists

Collaborations: M. Cazorla (Grenoble Institute of Neurosciences, Grenoble, France)

L. Lanfumey (Psychiatry and Neurosciences Center, Paris)

M. Hamon (Psychiatry and Neurosciences Center, Paris)

Observed structure-activity relationships indicate that:

· a position (position 4) of the B ring that is tolerant to the substitution with solubilizing moieties without altering in vitro potency;

· 2 out of the 3 amide bonds cannot be altered;

· ring A is very susceptible to chemical variations;

· the binding of ANA-12 to TrkB is stereoselective: (R)-isomer being 1000 times more potent than the (S)-isomer;

· a good permeation of the blood-brain barrier for some analogs (e.g. ANA-135)

2. FLT3 extracellular inhibitors

FLT3 is the receptor tyrosine kinase for the FL cytokine. Beyond its well established role in promoting cell differentiation in hematopoietic cells, we have discovered the unique property of FLT3 to behave as a main hub for triggering chronic pain upon nerve injury. Within the framework of a maturation program (INSERM-Transfert, SATT AxLR-Montpellier), one in silico hit (compound 11) previously identified to prevent the extracellular binding of the FL cytokine to its FLT3 tyrosine kinase receptor has been optimized by medicinal chemistry.

Proposed binding mode of the In silico Hit to the FLT3 receptor (tan surface)

Chemical variations on FLT3 inhibitors

We notably:

· enhanced in vitro potency (x40);

· switch from partial to total functional antagonism

· enhanced aqueous solubility(x400);

· selectivity for off-targets

· enhances metabolic stability

Optimized analogues (e.g. BDT001, BDT120, BDT169) exhibit strong anti-hyperalgesic properties in rodent models (CCI, SNL, SNI) of neuropathic pain, at low doses (2.5-5 mg/kg i.p.). The chemical series is protected by a patent (WO 2016016370 A1) and led to a start-up company (BIODOL Therapeutics, Montpellier), aiming at developing these compounds in clinical trials, for the treatment of chronic neuropathic pain.

Collaborations: J. Valmier (Institute of Neurosciences, Montpellier, France)

3. CD38 inhibitors

CD38 is a cell surface receptor acting as activation biomarker of immune cells. It is implicated in numerous cell signaling mechanisms among which survival of heart cells. Within the framework of a collaboration with SERVIER Laboratories, we have synthesized 59 analogs of our initial in silico hit (ICD4) and discovered potent human CD38 inhibitors (IC₅₀ = 900 nM). The most promising compounds are currently evaluated for their effects on cardiomyoctes.

We separately optimized another CD38 inhibitor selective for the Schistosoma mansoni receptor (see more )

Collaborations: A. Wagner, H. Steffner-Muller (UMR7199, Illkirch, France)

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Unravelling molecular mechanisms of actions

Our established expertise in molecular modelling, notably on G protein-coupled Receptors (GPCRs), led us to propose binding modes for many GPCR ligands which are validated by site-directed mutagenesis and in vitro binding/functional assays among which:

S1P1 receptor agonists ( Van Loenen et al., Eur. J. Pharmacol., 2011)
Mu opiate antagonists ( De Wachter et al., J. Med. Chem., 2011);
Fluorescent analogs of muscarininic M1 and M2 receptors (Daval et al., J. Med. Chem., 2012; Daval et al., Mol. Pharmacol., 2013), of the vasopressin V2 receptor Loison et al., J. Med. Chem., 2012), and of the dopamine D3 receptor (Hounsou et al., ACS Chem. Biol, 2015)
Antagonists of the non classical GPCR Smoothened ( Ruat et al., Trends Pharm. Sci., 2014; (Hoch et al., FASEB J.., 2015)

We have also been implied in deciphering the binding mode of siderophores (iron-chelating ligands) by the FptA transporter of Pseudomonas aeruginosa ( Brillet et al., J. Am. Chem. Soc., 2011; Noel et al., Org. Biomol. Chem., 2011; Noel et al., Bioorg. Med. Chem. Lett. J.., 2014)

In a long collaboration with the Pasteur Institute (B. Lagane, Dpt. of Virology), we have explained the the binding mode of the antiviral drug Maraviroc® to the chemokine CCR5 receptor antagonist; its allosteric nature ( style='color:blue;mso-themecolor:hyperlink'> Garcia-Perez et al., J. Biol. Chem., 2011; Garcia-Perez et al., J. Biol. Chem., 2011). We also have determined the influence of the V3 loop of the viral gp120 protein on the Maraviroc-induced resistance to VIH infection ( Garcia-Perez et al., Retrovirol., 2015 ).

We collaborate with Prof. R. Quinn (Griffith University, Brisbane, Autralia) to explain the cross-reactivity of natural products by biosynthetic enzymes and drug targets, thereby explaining why these compounds are a rich source of potential drug-candidates ( Kellenberger et al., Nat. Prod., 2011; Sturm et al., J. Chem. Info. Model., 2012; Sturm et al., Planta Med., 2015).

Collaborations: A.E. Alewijnse (Academic Medical Center, Amsterdam,The Netherlands.)

D. Tourwé (Vrije Universiteit, Brussels, Belgium)

J.L. Galzi, I. Schalk (UMR 7242 CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg)

T. Durroux, B. Mouillac, G. Guillon, J.P. Pin (Institut de Gémique Fonctionnelle , Montpellier, France)

M. Ruat (Alfred Fessard Institute of Neurobiology,Gif Sur Yvette, France)

B. Lagane, F. Arenzana-Seisdedos (Pasteur Institute, Paris)

R. Quinn (Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia.)