Melting points were measured on a Boetius melting point apparatus and were uncorrected. 1H NMR spectra were recorded on a Bruker DRX-500 instrument [working frequencies of 500.13 MHz (1H) and 125.76 MHz (13C)]. Chemical shifts were stated in parts per million (ppm) and referenced to the appropriate NMR solvent peaks. Spin-spin coupling constants (J) were reported in Hertz (Hz). Low resolution mass spectra (m/z) were recorded on a Finnigan MAT/INCOS 50 mass spectrometer at 70 eV using direct probe injection. Elemental analysis was performed on the automated Perkin-Elmer 2400 CHN microanalyzer. Flash chromatography was carried out on silica gel (Acros, 0.035–0.070 mm, 60 Å). TLC was performed on Merck 60 F254 plates. Solvents, 2-methyltriptamine, and acid chloroanhydrides were purchased from Chemical Block Ltd. (www.chemical-block.com) at the highest commercial quality and used as received. Compounds 1–74 (Supplementary Table S1) were purchased from Chemical Block Ltd. (www.chemical-block.com), where they were synthesized according to Scheme 1. Intermediate 2-methyltryptamines I were synthesized from arylhydrazine and 5-chloropenthanone-2 by Fisher-Grandberg reaction (Scheme 1). Further acylation of 2-methyltryptamines I using the respective chloroanhydrides of benzoic and heterocyclic acids afforded the target molecules 1–74 and specific inhibitor of Arp2/3 complex CK-666. Their purity and structure were further confirmed by ¹H NMR and mass spectrometry and elemental analysis (Supplementary Data Sheet S1).

A solution of Et₃N (3.06 g, 30.3 mmol) and 2-methyltryptamine (1.97 g, 10.1 mmol) in dry CH₂Cl₂ (30 ml) was stirred for 1 h at 20°C, cooled until 0°C, and then chloro-anhydride (11.5 mmol) in dry CH2Cl2 (10 ml) was added dropwise. The reaction mixture was stirred for 3 h at room temperature, washed with water, dried and evaporated. The product was separated by column chromatography (EtOAc/petroleum ether = 1/3, R _f = 0.3) and dried in vacuum (2 mm Hg) at 35–40°С to afford the target pure material.

The immortalized epithelial cell line from human breast, MCF10A was obtained from the Institut Curie collection of breast cell lines, organized and maintained by Thierry Dubois in Paris. MCF10A cells were cultured in DMEM/F12 medium (Gibco) supplemented with 5% horse serum (Sigma), 100 ng/ml cholera toxin (Sigma), 20 ng/ml epidermal growth factor (Sigma), 0.01 mg/ml insulin (Sigma), 500 ng/ml hydrocortisone (Sigma) and 100 U/ml penicillin/streptomycin (Gibco). B16-F1 mouse melanoma cells were obtained from Klemens Rottner (Technische Universität Braunschweig, Germany). B16-F1 cells were grown in DMEM supplemented with 10% fetal calf serum (Invitrogen) and 100 U/ml penicillin/streptomycin (Gibco). Cells were incubated in a humidified atmosphere with 5% CO₂.

Cell viability was assessed using the CellTiter 96^® AQueous One Solution Cell Proliferation kit (Promega) on a Multiscan Spectrum spectrophotometer (Thermo LifeSciences), with absorbance read at 490 nm.

For cell cycle progression using EdU, MCF10A cells were seeded in 384-well plates at a density of 800 cells per well. After spreading, cells were treated for 18 h with compounds in DMSO (final DMSO concentration did not exceed 0.5%). EdU from kit C10337 (ThermoFischer Scientific, Waltham, MA, United States) was then added to the cells at 10 μM and incubated for 2.5 h. Cells were fixed in 4% paraformaldehyde for 30 min at room temperature. Click-iT reaction was performed for 1 h at room temperature, protected from light, with 5 µM Alexa Fluor 488 azide in (100 mM Tris, 1 mM CuSO4, 50 mM Ascorbic Acid, pH 8.5). Nuclei were counterstained with Hoechst 33,342 (Thermo Fisher Scientific). Imaging and analysis were performed using the ImageXpress Micro XL High-Content Screening System (Molecular Devices LLC, San Jose, CA, United States). IC50 values were determined by sigmoidal curve fitting using GraphPad Prism six software.

Lyophilized compounds were resuspended with fresh DMSO from sealed vials (cell biology grade). Compounds, stored at +4°C, were used within a week. B16-F1 cells were seeded onto glass coverslips coated for 1 h with 25 μg/ml laminin (Sigma) in (50 mM Tris, 150 mM NaCl, pH 7.4). Tested compounds, CK-666 and its inactive control, CK-689 (N-(2-(1H-Indol-3-yl)ethyl)-2-methoxy-acetamide) (Merck) were added to cells for 1 h, then lamellipodia were promoted for 20 min in complete medium with AlCl₃ and NaF at the final concentration of 50 μM and 30 mM, respectively. Cell were then processed for immunofluorescence.

For the wound healing, B16-F1 cells were seeded onto 8-well Ibidi dishes coated with laminin, and grown to confluence. Wounds in the cell monolayer were obtained by scratching the monolayer with a pipet tip. Detached cells were immediately washed away and new medium containing the various compounds was added. Cells were then used for videomicroscopy.

Cells were fixed in 3.2% PFA on PBS, then quenched with 50 mM NH₄Cl and permeabilised with 0.5% Triton X-100. After blocking in 2% BSA cells were incubated with antibodies (1–5 μg/ml for the primary, 5 μg/ml for the secondary). Total actin in cells was visualized by phalloidin staining. Nuclei were stained with 0.3 μg/ml DAPI (Roche). Coverslips were mounted in Dako Fluorescence Mounting Medium (Agilent). For immunofluorescence, ARPC2 rabbit polyclonal antibody (Millipore, 07–227), Cortactin mouse monoclonal 4F11 (Millipore, 05–180) were used. Secondary goat anti-mouse and anti-rabbit antibodies conjugated with Alexa Fluor 555 and 647 respectively were from Life Technologies. Phalloidin conjugated with Alexa Fluor 488 was from Tebu-bio.

Videomicroscopy was performed on an inverted Axio Observer microscope (Zeiss) equipped with a Pecon Zeiss incubator XL multi S1 RED LS (Heating Unit XL S, Temp module, CO₂ module, Heating Insert PS and CO₂ cover), Definite focus module and a Hamamatsu camera C10600 Orca-R2. Phase contrast images were taken every 30 min for 24 h using the 10X/0.25 Plan-Apochromat air objective. For immunofluorescence, slides were observed and imaged with the 63X/1.4 Plan-Apochromat oil objective. Fluorophores were excited with the HBO 100 W lamp (Osram) installed in the HXP 120 Metal halide fluorescence light source (Zeiss).

Image analysis was performed in ImageJ or FIJI software. To measure wound healing, boundaries of the wound were drawn manually at different time points, then wound size was measured. A cell was counted as displaying a lamellipodium if a cortactin positive concave protrusion wider than the major diameter of the nucleus was displayed.

Actin was purified from rabbit muscle and was pyrenyl-labeled (Carlier et al., 1984; Malm, 1984). Arp2/3 was from Cytoskeleton, Inc. VCA domain of N-WASP was purified as previously described (Clainche et al., 2003). Pyrene-actin polymerization assays were performed as previously (Romero et al., 2007). Briefly, CaATP-actin was converted into MgATP-actin in (5 mM Tris, 0.2 mM ATP, 0.1 mM CaCl₂, 1 mM DTT, 1 mM MgCl₂, and 0.2 mM EGTA, pH 7.6) and kept on ice for no more than 1 h. Actin polymerization was monitored in (5 mM Tris, 50 mM KCl, 0.2 mM ATP, 0.1 mM CaCl₂, 1 mM DTT, 1 mM MgCl₂, 0.2 mM EGTA, pH 7.6) in the presence of 2% DMSO alone or 2% DMSO containing the appropriated compound concentration. The increase in fluorescence of 10% pyrenyl-labeled actin was monitored using a Safas spectrofluorimeter (λ_exc = 366 nm, λ_em = 407 nm). The maximum rate of actin polymerization was derived from the maximum slope of the polymerization curve multiplied by [total polymer]/(RFUmax—RFUmin) [total polymer] is the total actin minus the critical concentration (0.1 μM) and RFU, Relative Fluorescence Unit. The maximum elongation rates of actin polymerization were plotted as a function of the concentration of the different compounds. For CK-666, 59, 69 and 71, curves were fitted with the following equation to determine the IC50. M r a t e =     R m a x − R m a x − R m i n 1 + I C 50 ( C o m p o u n d   C o n c . ) where M_rate is the measured maximum rate of actin polymerization at a given compound concentration, R_max is the maximum rate of actin polymerization with no compound, and R_min is the maximum rate of actin polymerization at saturating concentration of compound.

The curve of compound 15 was fitted with a linear decay. The IC50 was determined at half inhibition of actin polymerization.

The procedure was described in detail in Semenova et al., 2018. Briefly, adult sea urchins, Paracentrotus lividus L (Echinidae), were collected from the Mediterranean Sea on the Cyprus coast and kept in an aerated seawater tank. Gametes were obtained by intracoelomic injection of 0.5 M KCl. Eggs were washed with filtered seawater and fertilized by adding drops of diluted sperm. Embryos were cultured at room temperature under gentle agitation with a motor-driven plastic paddle (60 rpm) in filtered seawater. Embryos were observed with a Biolam light microscope (LOMO, St. Petersburg, Russian Federation). For treatment with test compounds, 5 ml aliquots of embryo suspension were transferred to six-well plates and incubated at a concentration of 1,000–2,000 embryos/ml. For images, sedimented embryos were concentrated in the center of the well by gentle rotation of the culture plate, and 200 μl aliquots containing several hundred embryos were used to take pictures (up to 20 images from different fields). Embryos selected for Figure 4 were representative of the population.

Stock solutions of compounds were prepared in DMSO at 50–250 mM concentration followed by a 10-fold dilution with 96% EtOH. This procedure enhanced the solubility of the test compounds in the salty seawater. Maximal tolerated concentrations of DMSO and EtOH in the assay were determined to be 0.05 and 1%, respectively. Higher concentrations of either DMSO (>0.1%) or EtOH (>1%) caused nonspecific alterations and retardation of the sea urchin embryo development independent of the treatment stage. Maximum solubility of compounds 15, 59, 69, and 71 was about 5–20 mM in seawater, since visible crystals formed at higher concentrations.

The effects were assessed after exposure of fertilized eggs (8–15 min post fertilization, 45–55 min before the first mitotic cycle completion) to 2-fold decreasing concentrations of the compound. Embryonic development was monitored until the beginning of active feeding at four-arm pluteus stage (33–36 h postfertilization). Developmental abnormalities were estimated quantitatively as minimal effective concentration (MEC), resulting in inhibition of archenteron elongation or skeletal spicule formation.

Microphotographs were obtained using an AmScope binocular microscope with an MU500 digital camera (United Scopes LLC, Irvine, CA, United States). The embryos were immobilized with 5-[(6,7-dimethoxy-1,3-benzodioxol-5-yl)methyl]-3-(4-methoxyphenyl)-4,5-hydroisoxazole] at a concentration of 2 μM for 20 min (Semenova et al., 2008).

Experiments with sea urchin embryos fulfill the requirements of biological ethics: artificial spawning does not cause animal death, embryos develop outside the female organism, and both post spawned adult sea urchins and the excess of intact embryos were returned to the sea, their natural habitat.

The 2.48 Å resolution of crystal structure of bovine Arp2/3 complexed with CK-666 (Nolen et al., 2009) was retrieved from the PDB code 3UKR and optimized using the Protein Preparation Wizard in Maestro (Schrödinger, 2021) adding bond orders and hydrogen atoms to the crystal structure using the OPLS3e force field (Roos et al., 2019). Prime was used to fix missing residues or atoms in the protein. PROPKA was used to check for the protonation state of ionizable protein groups at pH 7.0. Hydrogen bonds were optimized through the reorientation of hydroxyl bonds, thiol groups, and amide groups. In the end, the system was minimized with a value of convergence of the RMSD of 0.3 Å. Ligands were prepared using LigPrep with the OPLS3e force field.

Induced-fit docking (IFD) models conformational changes induced by ligand binding (Sherman et al., 2006). The steps used are detailed in (Tutone et al., 2019; Allegra et al., 2021). The grid box for the binding site was built considering the co-crystallized ligand CK-666 as a centroid, while other parameters were kept as default. The most favorable binding poses of ligands in Arp2/3 complex were selected based on the IFD score and visual inspection of binding modes. Selected complexes were visualized using the Ligand Interactions module in Maestro to check interactions between ligands and residues of the ligand binding pocket.

In the chemical library of Chemical Block Ltd. 74 compounds featuring the same 2-methyl triptamine skeleton as the canonical Arp2/3 inhibitor CK-666 were identified. To efficiently screen these compounds, we took advantage of the recent observation that Arp2/3 activity is required for cell cycle progression in untransformed cells (Molinie et al., 2019). The Arp2/3 inhibitor CK-666 blocks MCF10A cells in G1 phase. This defect translates into a lack of incorporation of EdU, a thymidine analog, into DNA during its replication in S phase of mitotic cycle. EdU nuclear labeling can be easily scored using automated microscopy by click chemistry with Hoechst counterstaining of all nuclei (Supplementary Figure S1). We tested in parallel all compounds with concentration values ranging from 0.025 to 100 μM. Nine molecules 12, 15, 24, 30, 52, 59, 64, 69 and 71 were scored positive in this assay. They inhibited EdU incorporation more efficiently than CK-666 in a dose-dependent manner (Figure 1). Their chemical structures and rough IC₅₀ values are summarized in Table 1. The other compounds showed little or no effect.

Arp2/3 activity is most established to generate membrane protrusions, called lamellipodia, that mediate a type of cell motility, referred to as mesenchymal. Thus, the next step was to evaluate whether the nine selected compounds inhibited lamellipodium formation and cell migration. These assays are more demanding than monitoring cell cycle progression by EdU incorporation. B16-F1 murine melanoma cells, which are well known to form prominent lamellipodia, were chosen. These lamellipodia were further enhanced by treating cells with aluminium fluoride (Hahne et al., 2001). Control B16-F1 cells treated with 100 μM of the inactive CK-689 compound formed a single wide lamellipodium encompassing most cell perimeter. As expected, these lamellipodia contained polymerized actin, visualized by phalloidin staining, Arp2/3 complexes, detected by immunofluorescence of the ARPC2 subunit, and cortactin that stabilizes branched actin junctions (Figure 2A) (Gautreau et al., 2021). CK-666 at 100 μM concentration blocked lamellipodium formation almost completely (Figure 2B). All nine selected compounds also efficiently inhibited lamellipodium formation. Six of them, 15, 52, 59, 64, 69, 71, showed similar or higher activity compared to CK-666. Compounds 12, 30 and 24, were significantly less active than CK-666 (outside of the 1 S.D. range) and were excluded from further analysis. Compounds 52 and 64 were significantly toxic to B16-F1 cells, since they reduced the cell population by half or more (Figure 2C). They were therefore also excluded. The remaining four compounds, were evaluated in dose-dependent assays on lamellipodium formation (Figure 2D). At least two of them, compounds 15 and 71, were significantly more potent than CK-666, whereas compound 69 was similar to CK-666, and compound 59 was slightly less active than CK-666.

For direct assessment of cell migration, we used a wound healing assay, where B16-F1 cells migrate to a cell-free zone obtained by scratching cells out with a pipette tip. This assay was less sensitive than the direct counting of cells displaying lamellipodia, but it allowed to directly observe cell migration over time. At 100 µM concentration, compounds 71, 15, and to a lesser extent 59 induced cell rounding followed by detachment from the substrate (Supplementary Video S1). This effect was not observed for 15 and 59 at 25 µM concentration (Supplementary Video S2). Compounds 15 and 69 at 25 µM concentration, inhibited cell migration as efficiently as 100 µM CK-666 (Figure 2E). Compound 59 at 25 µM appeared more active than CK-666 at 100 µM and compound 71 at 25 µM concentration inhibited cell migration even more effectively, but still induced cell rounding at this concentration.

We next addressed whether compounds 15, 59, 69, and 71 inhibited Arp2/3 activity in vitro, as suggested by their effect on cell cycle progression and cell migration. To this end, we performed the classical fluorescence assay that monitors polymerization of actin coupled to pyrene. CK-666, but not CK-689, inhibited Arp2/3-mediated actin polymerization in a dose-dependent manner (Figure 3), in agreement with previous studies (Nolen et al., 2009; Hetrick et al., 2013). CK-666 displayed an IC₅₀ of 23 μM and reached 78% of Arp2/3 inhibition at saturation. In this in vitro assay, the CK-666 analogs were overall less active than CK-666 itself. Compound 69 displayed an IC₅₀ of 61 μM and reached 67% inhibition at saturation. IC₅₀ of compounds 59 and 71 were 180 and 539 μM, respectively, and saturation was not reached. Compound 15 reached 100% inhibition in a linear manner, unlike CK-666 and the other analogs. Its IC₅₀ was nonetheless 104 μM, higher than that of CK-666. Thus all four selected compounds were active against Arp2/3 in vitro although with different kinetic parameters than those of CK-666.

The effects of compounds 15, 59, 69, and 71 and standard Arp2/3 inhibitor CK-666 were examined using the sea urchin embryo model. Due to relatively large size and optical transparency of the embryos, this model allows for the direct monitoring of embryonic cell migration. Sea urchin gastrulation consists of two phases (Ettensohn, 1985). During the first one, primary mesenchyme cells (PMC) ingress into blastocoel in the vegetal pole and migrate to form ventrolateral clusters, where rudimental triradiate spicules appear (Figure 4). The second phase begins when the primary gut, the archenteron, reaches approximately its half-size. The secondary mesenchyme cells (SMC) emerging from the tip of archenteron pull the archenteron to the region of the future mouth.

According to literature, CK-666 at 100 μM concentration alters proper migration of PMC and formation of ventrolateral clusters with ensuing inhibition of spiculogenesis (Sepúlveda-ramírez et al., 2018). We studied the effect of CK-666 and its analogs 15, 59, 69, and 71 over a longer period, up to the four-arm mid-pluteus stage. Compounds 59 and 69 as well as CK-666 altered PMC migration resulting in the lack of ventrolateral clusters and spicules. In addition, they inhibited elongation of the archenteron at approximately half-size (Figure 4), suggesting a developmental blockade at the transition from the first to the second phase of gastrulation, probably because of SMC defective migration. However, malformed gastrulae remained alive and were able to swim up to 34–35 h post fertilization. Compounds 59 and 69 were more active than CK-666 in this assay, inducing the same morphogenic aberrations at roughly 5-fold lower concentrations (Table 2).

It should be noted that these compounds as wells as CK-666 up to 20–50 μM concentration did not affect cleavage and did not induce embryo spinning, typical effects of antimitotic microtubule destabilizing agents (Semenova et al., 2018). Beyond doubt, sea urchin embryo developmental alterations caused by CK-666 and the compound 59 and 69 were not caused by their side effect on another cytoskeletal system responsible for cell migration.

In contrast, compounds 15 and 71 induced nonspecific developmental abnormalities that were interpreted as systemic toxicity. At 5 μM concentration they suppressed plutei growth, whereas at 20 μM defective gastrulation was observed (Figure 4D). Due to low transparency of such gastrulae it was impossible to assess specific inhibitory effects related to PMC and SMC migration, such as inhibition of spicule formation and archenteron elongation.

In conclusion, in vivo, compounds 59 and 69 are Arp2/3 inhibitors with high potency and low toxicity.

Compounds 59 and 69 contain substituents in positions underexplored in previous studies (Nolen et al., 2009; Baggett et al., 2012; Hetrick et al., 2013). Therefore, to give flexibility to protein backbone and side chains, we used induced-fit docking (IFD) in the CK-666 binding site to allow ligand to adjust and optimize binding interactions with the Arp2/3 complex. The CK-666 binding site is at the interface between Arp2 and Arp3 subunits and CK-666 traps Arp2/3 in an inactive conformation (Nolen et al., 2009).

As a control, we first applied the IFD procedure to CK-666 itself. We obtained a docking score of -7.644. The indole NH of CK-666 formed a hydrogen bound with the side chain of the conserved Asp248^Arp2 and the amide oxygen of the CK-666 linker forms a hydrogen bound to the backbone NH of Ala203^Arp2 (Figure 5A). The indole ring formed CH-π interactions with Ser188^Arp3 and Leu246^Arp2. The C2-methyl group bound to Leu117^Arp3 and the aliphatic portion of Arg250^Arp2. In addition, o-fluorobenzene ring filled the hydrophobic pocket created by Leu117^Arp3, Thr119^Arp3, Tyr202^Arp2, Leu246^Arp2, and Ile252^Arp2, thus forming favorable interactions with the complex. All these predicted interactions of CK-666 were indeed observed in the co-crystal structure (Nolen et al., 2009).

Then the IFD procedure was applied to compound 59. The best IFD results engaged benzoyl tryptamine of 59 in similar interactions to that observed with CK-666 bound Arp2/3 complex. It is associated with a docking score of -11.473. The bulky benzyl group of 59 induced a slight movement of β12 and β13 strands of Arp2 to occupy the lipophilic pocket formed by Phe204^Arp2, Val213^Arp2, Ile216^Arp2, Tyr244^Arp2, Leu246^Arp2, and Ile252^Arp2 (Figure 5B). The ortho-fluoro group of CK-666 formed an intramolecular hydrogen bond with the NH of its amide group. This locked the benzene ring of CK-666 in a conformation required for its inhibitory activity. In contrast, the meta-bromine atom of 59 did not favor this conformation. Compound 59, however, can probably be debenzylated in vivo (Supplementary Scheme S1). Thus we performed IFD with the resulting metabolite, which provides a docking score of -8.361. The debenzylation yielded the C5 phenol hydroxyl group that might form two hydrogen bonds with Asp209^Arp2 and Thr212^Arp2 (Figure 5C).

The IFD of 69 gave a docking score of -7.975. The C7-chlorine group moved a loop between β12 and β13 strands of Arp2 and formed weak interactions with Pro247^Arp2. A water molecule mediated contact between sulfonamide oxygen and the backbone C=O of Leu117^Arp3. N-methyl of tertiary sulfonamide bound to Tyr202^Arp2, Ile252^Arp2, and Lys253^Arp2 (Figure 5D). In conclusion, the best hits, 59 and 69, probably bound to the same binding site as CK-666, but with significant variations.