Identification of acylthiourea derivatives as potent Plk1 PBD inhibitors

Identification of naphthalimide-derivatives as novel PBD-targeted polo-like kinase 1 inhibitors with efficacy in drug-resistant lung cancer cells

Targeting polo-box domain (PBD) small molecule for polo-like kinase 1 (PLK1) inhibition is a viable alternative to target kinase domain (KD), which could avoid pan-selectivity and dose-limiting toxicity of ATP-competitive inhibitors. However, their efficacy in these settings is still low and inaccessible to clinical requirement. Herein, we utilized a structure-based high-throughput virtual screen to find novel chemical scaffold capable of inhibiting PLK1 via targeting PBD and identified an initial hit molecule compound 1a. Based on the lead compound 1a, a structural optimization approach was carried out and several series of derivatives with naphthalimide structural motif were synthesized. Compound 4Bb was identified as a new potent PLK1 inhibitor with a KD value of 0.29 μM. 4Bb could target PLK1 PBD to inhibit PLK1 activity and subsequently suppress the interaction of PLK1 with protein regulator of cytokinesis 1 (PRC1), finally leading to mitotic catastrophe in drug-resistant lung cancer cells. Furthermore, 4Bb could undergo nucleophilic substitution with the thiol group of glutathione (GSH) to disturb the redox homeostasis through exhausting GSH. By regulating cell cycle machinery and increasing cellular oxidative stress, 4Bb exhibited potent cytotoxicity to multiple cancer cells and drug-resistant cancer cells. Subcutaneous and oral administration of 4Bb could effectively inhibit the growth of drug-resistant tumors in vivo, doubling the survival time of tumor bearing mice without side effects in normal tissues. Thus, our study offers an orally-available, structurally-novel PLK1 inhibitor for drug-resistant lung cancer therapy.

Discovery of Novel Pyrazole Acyl Thiourea Skeleton Analogue as Potential Herbicide Candidates

To discover novel transketolase (TKL, EC 2.2.1.1) inhibitors with potential herbicidal applications, a series of pyrazole acyl thiourea derivatives were designed based on a previously obtained pyrazolamide acyl lead compound, employing a scaffold hopping strategy. The compounds were synthesized, their structures were characterized, and they were evaluated for herbicidal activities. The results indicate that 7a exhibited exceptional herbicidal activity against Digitaria sanguinalis and Amaranthus retroflexus at a dosage of 90 g ai/ha, using the foliar spray method in a greenhouse. This performance is comparable to that of commercial products, such as nicosulfuron and mesotrione. Moreover, 7a showed moderate growth inhibitory activity against the young root and stem of A. retroflexus at 200 mg/L in the small cup method, similar to that of nicosulfuron and mesotrione. Subsequent mode-of-action verification experiments revealed that 7a and 7e inhibited Setaria viridis TKL (SvTKL) enzyme activity, with IC50 values of 0.740 and 0.474 mg/L, respectively. Furthermore, they exhibited inhibitory effects on the Brassica napus acetohydroxyacid synthase enzyme activity. Molecular docking predicted potential interactions between these (7a and 7e) and SvTKL. A greenhouse experiment demonstrated that 7a exhibited favorable crop safety at 150 g ai/ha. Therefore, 7a is a promising herbicidal candidate that is worthy of further development.

Identification of PLK1-PBD Inhibitors from the Library of Marine Natural Products: 3D QSAR Pharmacophore, ADMET, Scaffold Hopping, Molecular Docking, and Molecular Dynamics Study

PLK1 is found to be highly expressed in various types of cancers, but the development of inhibitors for it has been slow. Most inhibitors are still in clinical stages, and many lack the necessary selectivity and anti-tumor effects. This study aimed to create new inhibitors for the PLK1-PBD by focusing on the PBD binding domain, which has the potential for greater selectivity. A 3D QSAR model was developed using a dataset of 112 compounds to evaluate 500 molecules. ADMET prediction was then used to select three molecules with strong drug-like characteristics. Scaffold hopping was employed to reconstruct 98 new compounds with improved drug-like properties and increased activity. Molecular docking was used to compare the efficient compound abbapolin, confirming the high-activity status of [(14S)-14-hydroxy-14-(pyridin-2-yl)tetradecyl]ammonium,[(14S)-15-(2-furyl)-14-hydroxypentadecyl]ammonium and [(14S)-14-hydroxy-14-phenyltetradecyl]ammonium. Molecular dynamics simulations and MMPBSA were conducted to evaluate the stability of the compounds in the presence of proteins. An in-depth analysis of [(14S)-15-(2-furyl)-14-hydroxypentadecyl]ammonium and [(14S)-14-hydroxy-14-phenyltetradecyl]ammonium identified them as potential candidates for PLK1 inhibitors.

Inhibitors of the PLK1 polo-box domain: drug design strategies and therapeutic opportunities in cancer

INTRODUCTION

Polo Like Kinase 1 (PLK1) is a key regulator of mitosis and its overexpression is frequently observed in a wide variety of human cancers, while often being associated with poor survival rates. Therefore, it is considered a potential and attractive target for cancer therapeutic development. The Polo like kinase family is characterized by the presence of a unique C terminal polobox domain (PBD) involved in regulating kinase activity and subcellular localization. Among the two functionally essential, druggable sites with distinct properties that PLK1 offers, targeting the PBD presents an alternative approach for therapeutic development.

AREAS COVERED

Significant progress has been made in progressing from the peptidic PBD inhibitors first identified, to peptidomimetic and recently drug-like small molecules. In this review, the rationale for targeting the PBD over the ATP binding site is discussed, along with recent progress, challenges, and outlook.

EXPERT OPINION

The PBD has emerged as a viable alternative target for the inhibition of PLK1, and progress has been made in using compounds to elucidate mechanistic aspects of activity regulation and in determining roles of the PBD. Studies have resulted in proof of concept of in vivo efficacy suggesting promise for PBD binders in clinical development.

Polo-like Kinase 1 Inhibitors in Human Cancer Therapy: Development and Therapeutic Potential

Polo-like kinase 1 (PLK1) plays an important role in a variety of cellular functions, including the regulation of mitosis, DNA replication, autophagy, and the epithelial-mesenchymal transition (EMT). PLK1 overexpression is often associated with cell proliferation and poor prognosis in cancer patients, making it a promising antitumor target. To date, at least 10 PLK1 inhibitors (PLK1i) have been entered into clinical trials, among which the typical kinase domain (KD) inhibitor BI 6727 (volasertib) was granted "breakthrough therapy designation" by the FDA in 2013. Unfortunately, many other KD inhibitors showed poor specificity, resulting in dose-limiting toxicity, which has greatly impeded their development. Researchers recently discovered many PLK1i with higher selectivity, stronger potency, and better absorption, distribution, metabolism, and elimination (ADME) characteristics. In this review, we emphasize the structure-activity relationships (SARs) of PLK1i, providing insights into new drugs targeting PLK1 for antitumor clinical practice.

Novel Macrocyclic Peptidomimetics Targeting the Polo-Box Domain of Polo-Like Kinase 1

The polo-box domain (PBD) of Plk1 is a promising target for cancer therapeutics. We designed and synthesized novel phosphorylated macrocyclic peptidomimetics targeting PBD based on acyclic phosphopeptide PMQSpTPL. The inhibitory activities of 16e on Plk1-PBD is >30-fold higher than those of PMQSpTPL. Both 16a and 16e possess excellent selectivity for Plk1-PBD over Plk2/3-PBD. Analysis of the cocrystal structure of Plk1-PBD in complex with 16a reveals that the 3-(trifluoromethyl)benzoyl group in 16a interacts with Arg516 through a π-stacking interaction. This π-stacking interaction, which has not been reported previously, provides insight into the design of novel and potent Plk1-PBD inhibitors. Furthermore, 16h, a PEGlyated macrocyclic phosphopeptide derivative, induces Plk1 delocalization and mitotic failure in HeLa cells. Also, the number of phospho-H3-positive cells in a zebrafish embryo increases in proportion to the amount of 16a. Collectively, the novel macrocyclic peptidomimetics should serve as valuable templates for the design of potent and novel Plk1-PBD inhibitors.

Single-Crystal Investigation, Hirshfeld Surface Analysis, and DFT Study of Third-Order NLO Properties of Unsymmetrical Acyl Thiourea Derivatives

In the current research work, unsymmetrical acyl thiourea derivatives, 4-((3-benzoylthioureido)methyl)cyclohexane-1-carboxylic acid (BTCC) and methyl 2-(3-benzoylthioureido)benzoate (MBTB), have been synthesized efficiently. The structures of these crystalline thioureas were unambiguously confirmed by single-crystal diffractional analysis. The crystallographic investigation showed that the molecular configuration of both compounds is stabilized by intramolecular N-H···O bonding. The crystal packing of BTCC is stabilized by strong N-H···O bonding and comparatively weak O-H···S, C-H···O, C-H···π, and C-O···π interactions, whereas strong N-H···O bonding and comparatively weak C-H···O, C-H···S, and C-H···π interactions are responsible for the crystal packing of MBTB. The noncovalent interactions that are responsible for the crystal packing are explored by the Hirshfeld surface analysis for both compounds. The void analysis is performed to find the quantitative strength of crystal packing in both compounds. Additionally, state-of-the-art applied quantum chemical techniques are used to further explore the structure-property relationship in the above-entitled molecules. The optimization of molecular geometries showed a reasonably good correlation with their respective experimental structures. Third-order nonlinear optical (NLO) polarizability calculations were performed to see the advanced functional application of entitled compounds as efficient NLO materials. The average static γ amplitudes are found to be 27.30 × 10^-36 and 102.91 × 10^-36 esu for the compounds BTCC and MBTB, respectively. The γ amplitude of MBTB is calculated to be 3.77 times larger, which is probably due to better charge-transfer characteristics in MBTB. The quantum chemical analysis in the form of 3-D plots was also performed for their frontier molecular orbitals and molecular electrostatic potentials for understanding charge-transfer characteristics. We believe that the current investigation will not only report the new BTCC and MBTB compounds but also evoke the interest of the materials science community in their potential use in NLO applications.

Synthesis of benzamide derivatives with thiourea-substituted benzenesulfonamides as carbonic anhydrase inhibitors

The novel compounds with the chemical structure of N-({4-[N'-(substituted)sulfamoyl]phenyl}carbamothioyl)benzamide (1a-g) and 4-fluoro-N-({4-[N'-(substituted)sulfamoyl]phenyl}carbamothioyl)benzamide (2a-g) were synthesized as potent and selective human carbonic anhydrase (hCA) I and hCA II candidate inhibitors. The aryl part was changed to sulfacetamide, sulfaguanidine, sulfanilamide, sulfathiazole, sulfadiazine, sulfamerazine, and sulfametazine. The K_i values of compounds 1a-g were in the range of 20.73 ± 4.32 to 59.55 ± 13.07 nM (hCA I) and 5.69 ± 0.43 to 44.81 ± 1.08 nM (hCA II), whereas the K_i values of compounds 2a-g were in the range of 13.98 ± 2.57 to 75.74 ± 13.51 nM (hCA I) and 8.15 ± 1.5 to 49.86 ± 6.18 nM (hCA II). Comparing the K_i values of the final compounds and acetazolamide, compound 1c with the sulfanilamide moiety (K_i  = 5.69 ± 0.43 nM, 8.8 times) and 2f with the sulfamerazine moiety (K_i  = 8.15 ± 1.5 nM, 6.2 times) demonstrated promising and selective inhibitory effects against the hCA II isoenzyme, the main target protein in glaucoma. Furthermore, compounds 1d (K_i  = 20.73 ± 4.32, 4 times) and 2d (K_i  = 13.98 ± 2.57, 5.9 times), which have the sulfathiazole moiety, were found as potent hCA I inhibitors. Compounds 1c and 2f can be considered as the lead compounds determined in the present study, which can be investigated further to alleviate glaucoma symptoms.

Discovery of Targeted Covalent Natural Products against PLK1 by Herb-Based Screening

Natural products (NPs) are a rich source of drug discovery, and some of them act by covalently binding to the targets. Recently, targeted covalent natural product (TCNP) design has gained considerable attention since this approach offers significant benefits in improving biological efficacy and decreasing the off-target side effects. However, most of the known TCNPs were discovered by chance. Rational approaches for a systematic screen of TCNPs are much needed. Here, we developed a combined computational and experimental approach to carry out herb-based screening to identify TCNPs against proper cysteine residues in the target proteins. The herb-based TCNP screening approach (HB-TCNP) starts from a druggable pocket and cysteine residue prediction, followed by virtual screening of a covalent NP database and herb-based mapping to identify candidate herbs for experimental validation. Herbs with time-dependent activity are selected, and their NPs are experimentally tested to further screen covalent NPs. We have successfully applied HB-TCNP to screen anti-PLK1 herbs and NPs with high efficacy. Cys67 and Cys133 in the ATP binding pocket of PLK1 were used in the search. Five herbs were tested and exhibited PLK1 inhibition activity to some extent, among which Scutellaria baicalensis showed the most potent activity with time dependency. Further experimental studies showed that the main active compounds in Scutellaria baicalensis, baicalein and baicalin, covalently bind PLK1 through Cys133. Our study provided an efficient way to rationally design TCNPs and to make better use of herb medicines. The Cys133 residue in PLK1 serves as a novel covalent site for further drug discovery against PLK1.

Discovery of a Potent PLK1-PBD Small-Molecule Inhibitor as an Anticancer Drug Candidate through Structure-Based Design

Polo-box domain of polo-like kinase 1 (PLK1-PBD) has a pivotal role in cell proliferation and could be implicated as a potential anticancer target. Although some small-molecule inhibitors have been developed, their clinical application has been restricted by the poor selectivity. Therefore, there is an urgent need to develop effective PLK1-PBD inhibitors. Herein, we have developed a virtual screening protocol to find PLK1-PBD inhibitors by using combination of structure-based pharmacophore modeling and molecular docking. This protocol was successfully applied to screen PLK1-PBD inhibitors from specs database. MTT assay indicated that five screened hits suppressed the growth of HeLa cells. Particularly, hit-5, as a selective PLK1 inhibitor targeting PLK1-PBD, significantly inhibited the progression of HeLa cells-derived xenograft, with no obvious side effects. This work demonstrates that hit-5 may be a potential anticancer agent.

Discovery of Inhibitors of Aurora/PLK Targets as Anticancer Agents

Aurora and polo-like kinases control the G2/M phase in cell mitosis, which are both considered as crucial targets for cancer cell proliferations. Here, naphthalene-based Aurora/PLK coinhibitors as leading compounds were designed through in silico approach, and a total of 36 derivatives were synthesized. One candidate (AAPK-25) was selected under in vitro cell based high throughput screening with an IC50 value = 0.4 μM to human colon cancer cell HCT-116. A kinome scan assay showed that AAPK-25 was remarkably selective to both Aurora and PLK families. The relevant genome pathways were also depicted by microarray based gene expression analysis. Furthermore, validated from a set of in vitro and in vivo studies, AAPK-25 significantly inhibited the development of the colon cancer growth and prolonged the median survival time at the end of the administration (p < 0.05). To sum up, AAPK-25 has a great potential to be developed for a chemotherapeutic agent in clinical use.

Structural insights into the inhibitor binding and new inhibitor design to Polo-like kinase-1 Polo-box domain using computational studies

Polo box domain (PBD) from Polo-Like Kinase-1 (PLK-1) a cell cycle regulator is one of the important non-kinase targets implicated in various cancers. The crystal structure of PLK-1 PBD bound to phosphopeptide inhibitor is available and acylthiourea derivatives have been reported as potent PBD inhibitors. In this work, structure and ligand-based pharmacophore methods have been used to identify new PBD inhibitors. The binding of acylthiourea analogs and new inhibitors to PBD were assessed using molecular docking and molecular dynamics simulations to understand their binding interactions, investigate the complex stability and reveal the molecular basis for inhibition. This study provides the binding free energies and residue-wise contributions to decipher the essential interactions in the protein-inhibitor complementarity for complex formation and the design of new PBD inhibitors with better binding. Communicated by Ramaswamy H. Sarma.

Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

There are many multidomain allosteric proteins where an allosteric signal at the allosteric domain modifies the activity of the functional domain. Intrinsically disordered regions (linkers) are widely involved in this kind of regulation process, but the essential role they play therein is not well understood. Here, we investigated the effect of linkers in stabilizing the open or the closed states of multidomain proteins using combined thermodynamic deduction and coarse-grained molecular dynamics simulations. We revealed that the influence of linker can be fully characterized by an effective local concentration [B]₀ . When K_d is smaller than [B]₀ , the closed state would be favored; while the open state would be preferred when K_d is larger than [B]₀ . We used four protein systems with markedly different domain-domain binding affinity and structural order/disorder as model systems to understand the relationship between [B]₀ and the linker length as well as its flexibility. The linker length is the main practical determinant of [B]₀ . [B]₀ of a flexible linker with 40-60 residues was determined to be in a narrow range of 0.2-0.6 mM, while a too short or too long length would dramatically decrease [B]₀ . With the revealed [B]₀ range, the introduction of a flexible linker makes the regulation of weakly interacting partners possible.

Stereoselective synthesis of a phosphonate pThr mimetic via palladium-catalyzed γ-C(sp3)–H activation for peptide preparation

We report a facile and efficient synthetic strategy toward a CH₂-substituted phosphonate pThr mimetic and its application in phosphopeptide inhibitor synthesis.