Synthesis and biological evaluation of pyrimidine derivatives as novel human Pin1 inhibitors

A novel μ3-CO3 bridged linear polymeric Cu-complex ([Cu3(DMAP)8(μ3-CO3)2]I2) n ·xH2O: synthesis, characterization and catalytic applications in the synthesis of phenoxypyrimidines and arylthiopyrimidines via C-O and C-S cross-coupling reactions

This manuscript reports on the synthesis and characterization of a new polymeric copper complex ([Cu3(DMAP)8(μ3-CO3)2]I2) n ·xH2O and its successful application in C-O and C-S cross coupling reactions for the synthesis of biologically important phenoxypyrimidine and arylthiopyrimidine scaffolds. In an attempt to synthesize [Cu(DMAP)4I]I by adopting a procedure reported by Roy et al. with slight modification, the authors discovered a new polymeric Cu-complex that contains μ3-CO3 bridges. The polymeric linear structure of the complex was established using single crystal X-ray analysis. FT-IR, UV-vis and DSC studies were also performed on the polymeric complex. This novel polymeric Cu-complex was found to efficiently catalyse C-O/C-S cross coupling reactions between chloropyrimidines and phenols/thiophenols in an aqueous medium within a short reaction time, delivering their corresponding phenoxypyrimidines and arylthiopyrimidines. Using this protocol, 22 phenoxypyrimidines and 6 arylthiopyrimidines were successfully synthesized. The synthesized novel compounds were well characterized using 1H and 13C NMR spectroscopy and HRMS analysis and were screened for their drug-likeness properties using the SwissADME webtool.

Recent advances of Pin1 inhibitors as potential anticancer agents

Pin1 (proline isomerase peptidyl-prolyl isomerase NIMA-interacting-1), as a member of PPIase family, catalyzes cis-trans isomerization of pThr/Ser-Pro amide bonds of its substrate proteins, further regulating cell proliferation, division, apoptosis, and transformation. Pin1 is overexpressed in various cancers and is positively correlated with tumor initiation and progression. Pin1 inhibition can effectively reduce tumor growth and cancer stem cell expansion, block metastatic spread, and restore chemosensitivity, suggesting that targeting Pin1 may be an effective strategy for cancer treatment. Considering the promising therapeutic effects of Pin1 inhibitors on cancers, we herein are intended to comprehensively summarize the reported Pin1 inhibitors, mainly highlighting their structures, biological functions and binding modes, in hope of providing a reference for the future drug discovery.

Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities

Proline isomerization, the process of interconversion between the cis- and trans-forms of proline, is an important and unique post-translational modification that can affect protein folding and conformations, and ultimately regulate protein functions and biological pathways. Although impactful, the importance and prevalence of proline isomerization as a regulation mechanism in biological systems have not been fully understood or recognized. Aiming to fill gaps and bring new awareness, we attempt to provide a wholistic review on proline isomerization that firstly covers what proline isomerization is and the basic chemistry behind it. In this section, we vividly show that the cause of the unique ability of proline to adopt both cis- and trans-conformations in significant abundance is rooted from the steric hindrance of these two forms being similar, which is different from that in linear residues. We then discuss how proline isomerization was discovered historically followed by an introduction to all three types of proline isomerases and how proline isomerization plays a role in various cellular responses, such as cell cycle regulation, DNA damage repair, T-cell activation, and ion channel gating. We then explore various human diseases that have been linked to the dysregulation of proline isomerization. Finally, we wrap up with the current stage of various inhibitors developed to target proline isomerases as a strategy for therapeutic development.

Copper-Catalyzed Direct Syntheses of Phenoxypyrimidines from Chloropyrimidines and Arylboronic Acids: A Cascade Avenue and Unconventional Substrate Pairs

This letter describes the first synthetic methodology for phenoxypyrimidines that avoids the direct use of phenols or their salts. In contrast to the general trend of delivering Suzuki-Miyaura cross-coupling products in reactions between aryl or alky halides and arylboronic acids, the substrate pairs used herein (chloropyrimidines and arylboronic acids) led to C-O bond formation under the reaction conditions. In total, 25 phenoxypyrimidines were successfully synthesized using the described protocol, 6 of which had a structural resemblance to etravirine.

Copper-Catalyzed C-N Bond Cleavage: Synthesis of N-Sulfonylformamidines from N-( 2-pyridinylmethyl)benzenesulfonamides

AIMS

Find an innovative approach to synthesizing N-sulfonylformamidines from new N source.

BACKGROUND

N-sulfonylamidines have gained considerable attention from school and industry because of unique bioactivity. Since Pinner's strategy, expanding the synthesis methods of N-sulfonylamidines has been the goal of many organic chemists over the past decades. Beside of the crash reaction conditions and the participation of undesirable reagents, the production of N-sulfonylamidines commonly required unstable ammonia and azides as the source of nitrogen which hindered the further development and application of N-sulfonylamidine derivatives.

OBJECTIVE

Find a stable N source to replace NaN3 or NH3 to synthesis N-sulfonylamidines.

METHOD

Firstly, N-( 2-pyridinylmethyl)benzenesulfonamides were smoothly synthesized via 2-pyridinemethanamine and sulfonyl chlorides. Then the reaction conditions of N-(2-pyridinylmethyl)benzenesulfonamides and N,N-dimethylformamide dimethyl acetal(DMF-DMA) were screened and optimized: the reaction was processed in glycol at 80 ℃ for 8 hours with the addition of 5 mol% Cu(OAc)2·H2O as catalyst.

RESULT

Taking the advantage of pyridin-2-ylmethyl, a scope of N-Sulfonylformamidines were synthesized from those N-(2-pyridinylmethyl)benzenesulfonamides under copper-catalyzed C-N bond cleavage.

CONCLUSION

This ready synthetic method will be more a promising inspiration of bioactive compound synthesis and drug development than of an innovative approach to synthesizing N-sulfonylformamidines.

Computer-Aided Drug Design Applied to Secondary Metabolites as Anticancer Agents

Computer-Aided Drug Design (CADD) techniques have garnered a great deal of attention in academia and industry because of their great versatility, low costs, possibilities of cost reduction in in vitro screening and in the development of synthetic steps; these techniques are compared with highthroughput screening, in particular for candidate drugs. The secondary metabolism of plants and other organisms provide substantial amounts of new chemical structures, many of which have numerous biological and pharmacological properties for virtually every existing disease, including cancer. In oncology, compounds such as vimblastine, vincristine, taxol, podophyllotoxin, captothecin and cytarabine are examples of how important natural products enhance the cancer-fighting therapeutic arsenal. In this context, this review presents an update of Ligand-Based Drug Design and Structure-Based Drug Design techniques applied to flavonoids, alkaloids and coumarins in the search of new compounds or fragments that can be used in oncology. A systematical search using various databases was performed. The search was limited to articles published in the last 10 years. The great diversity of chemical structures (coumarin, flavonoids and alkaloids) with cancer properties, associated with infinite synthetic possibilities for obtaining analogous compounds, creates a huge chemical environment with potential to be explored, and creates a major difficulty, for screening studies to select compounds with more promising activity for a selected target. CADD techniques appear to be the least expensive and most efficient alternatives to perform virtual screening studies, aiming to selected compounds with better activity profiles and better "drugability".

Targeting Pin1 for Modulation of Cell Motility and Cancer Therapy

Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) specifically binds and isomerizes the phosphorylated serine/threonine-proline (pSer/Thr-Pro) motif, which leads to changes in protein conformation and function. Pin1 is widely overexpressed in cancers and plays an important role in tumorigenesis. Mounting evidence has revealed that targeting Pin1 is a potential therapeutic approach for various cancers by inhibiting cell proliferation, reducing metastasis, and maintaining genome stability. In this review, we summarize the underlying mechanisms of Pin1-mediated upregulation of oncogenes and downregulation of tumor suppressors in cancer development. Furthermore, we also discuss the multiple roles of Pin1 in cancer hallmarks and examine Pin1 as a desirable pharmaceutical target for cancer therapy. We also summarize the recent progress of Pin1-targeted small-molecule compounds for anticancer activity.

Design, synthesis and biological evaluation of novel thiazole-based derivatives as human Pin1 inhibitors

Pin1 is a peptidyl prolyl cis-trans isomerase (PPIase) and inhibiting Pin1 is a potential way for discovering anti-tumor agents. With an aim to find potent Pin1 inhibitors with a novel scaffold, a series of thiazole derivatives with an alicyclic heterocycles on the 2-position were designed, synthesized and tested against human Pin1. Compound 9p bearing a 2-oxa-6-azaspiro [3,3] heptane moiety on the thiazole scaffold was identified as the most potent Pin1 inhibitor of this series with an IC₅₀ value of 0.95 μM. The structure-activity relationship (SAR) and molecular modeling study indicated that introducing an alicyclic ring with an H-bond acceptor would be a viable way to improve the binding affinity.

One Reacts as Two: Applications of N-Isocyaniminotriphenylphosphorane in Diversity-Oriented Synthesis

N-Isocyaniminotriphenylphosphorane (NIITP) is a functionalized isonitrile that has been extensively applied in a variety of organic reactions during the last two decades. This Review summarizes the most important applications in organic synthesis of this versatile reactant, with the focus posed on mechanistic and methodological aspects allowing the generation of molecular diversity. NIITP combines the reactivity of isonitriles with that of phosphoranes to enable chemical transformations employed in the construction of compound libraries. Here, we cover from the initial applications of NIITP in the Nef isocyanide reaction to further derivations that render a variety of heterocyclic scaffolds. The presence of the isonitrile moiety in this singular compound makes possible the double addition of nucleophiles and electrophiles, which followed by inter(intra)molecular aza-Wittig type transformations enable several multicomponent and tandem processes. In particular, we stress the impact of NIITP in oxadiazole chemistry, from the early two-component transformations to recent examples of multicomponent reactions that take place in the presence of suitable electrophiles. In addition, we briefly describe the role of NIITP chemistry in generating skeletal and conformational diversity in cyclic peptides. The reaction of NIITP with alkynes is thoroughly revised, with particular emphasis on silver-catalyzed processes that have been developed in the last years. Biomedicinal applications of some reaction products are also mentioned along with a perspective of future applications of this reactant.

Function of PIN1 in Cancer Development and Its Inhibitors as Cancer Therapeutics

Peptidyl-prolyl isomerase (PIN1) specifically binds and isomerizes the phosphorylated serine/threonine-proline (pSer/Thr-Pro) motif, which results in the alteration of protein structure, function, and stability. The altered structure and function of these phosphorylated proteins regulated by PIN1 are closely related to cancer development. PIN1 is highly expressed in human cancers and promotes cancer as well as cancer stem cells by breaking the balance of oncogenes and tumor suppressors. In this review, we discuss the roles of PIN1 in cancer and PIN1-targeted small-molecule compounds.

Computational Molecular Modeling of Pin1 Inhibition Activity of Quinazoline, Benzophenone, and Pyrimidine Derivatives

Pin1 (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1) is directly involved in cancer cell-cycle regulation because it catalyses the cis-trans isomerization of prolyl amide bonds in proteins. In this sense, a modeling evaluation of the inhibition of Pin1 using quinazoline, benzophenone, and pyrimidine derivatives was performed by using multilinear, random forest, SMOreg, and IBK regression algorithms on a dataset of 51 molecules, which was divided randomly in 78% for the training and 22% for the test set. Topological descriptors were used as independent variables and the biological activity (pIC50) as a dependent variable. The most robust individual model contained 9 features, and its predictive capability was statistically validated by the correlation coefficient for adjusting, 10-fold cross validation, test set, and bootstrapping with values of 0.910, 0.819, 0.841, and 0.803, respectively. In order to improve the prediction of the pIC50 values, the aggregation of the individual models was performed through the construction of an ensemble, and the most robust one was constructed by two individual models (LR3 and RF1) by applying the IBK algorithm, and a substantial improvement in predictive performance is reflected in the values of R2ADJ = 0.982, Q2CV = 0.962, and Q2EXT = 0.918. Mean square errors <0.165 and good fitting between calculated and experimental pIC50 values suggest a robustness on the prediction of pIC50. Regarding the docking simulation, a binding affinity between the molecules and the active site for the Pin1 inhibition into the protein (3jyj) was estimated through the calculation of the binding free energy (BE), with values in the range of −5.55 to −8.00 kcal/mol, implying a stabilizing interaction molecule receptor. The ligand interaction diagrams between the drugs and amino acid in the binding site for the three most active compounds denoted a good wrapper of these organic compounds into the protein mainly by polar amino acids.

Structure-Based Design of Novel Benzimidazole Derivatives as Pin1 Inhibitors

Peptidyl-prolyl cis/trans isomerase Pin1 plays a key role in amplifying and translating multiple oncogenic signaling pathways during oncogenesis. The blockade of Pin1 provided a unique way of disrupting multiple oncogenic pathways and inducing apoptosis. Aiming to develop potent Pin1 inhibitors, a series of benzimidazole derivatives were designed and synthesized. Among the derivatives, compounds 6h and 13g showed the most potent Pin1 inhibitory activity with IC₅₀ values of 0.64 and 0.37 μM, respectively. In vitro antiproliferative assay demonstrated that compounds 6d, 6g, 6h, 6n, 6o and 7c exhibited moderate antiproliferative activity against human prostate cancer PC-3 cells. Taken together, these unique benzimidazole derivatives exhibited great potential to be further explored as potent Pin1 inhibitors with improved potency.

Synthesis and Evaluation of 3-Substituted-4-(quinoxalin-6-yl) Pyrazoles as TGF-β Type I Receptor Kinase Inhibitors

The transforming growth factor-β (TGF-β), in which overexpression has been associated with various diseases, has become an attractive molecular target for the treatment of cancers. Thirty-two quinoxaline-derivatives of 3-substituted-4-(quinoxalin-6-yl) pyrazoles 14a–d, 15a–d, 16a–d, 17a–d, 18a–d, 19a–d, 25a, 25b, 25d, 26a, 26b, 26d, 27b, and 27d were synthesized and evaluated for their activin TGF-β type I receptor kinase and p38α mitogen activated protein (MAP) kinase inhibitory activity in enzymatic assays. Among these compounds, the most active compound 19b inhibited TGF-β type I receptor kinase phosphorylation with an IC₅₀ value of 0.28 µM, with 98% inhibition at 10 µM. Compound 19b also had good selectivity index of >35 against p38α MAP kinase, with 9.0-fold more selective than clinical candidate, compound 3 (LY-2157299). A molecular docking study was performed to identify the mechanism of action of the synthesized compounds and their good binding interactions were observed. ADMET prediction of good active compounds showed that these ones possess good pharmacokinetics and drug-likeness behavior.

Design, synthesis and biological evaluation of benzimidazole derivatives as novel human Pin1 inhibitors

In this work, a series of novel benzimidazole derivatives were designed and synthesized as Pin1 inhibitors. Protease-coupled assay was used to investigate the Pin1 inhibitory potency of all synthesized compounds. Thirteen of them showed preferable Pin1 inhibitory effects with IC₅₀ values lower than 5 μM, and 12a, 15b, 15d and 16c exhibited the most promising Pin1 inhibitory activity at low micromolar level (0.33-1.00 μM) than the positive control compound Juglone. Flow cytometry results showed that treating PC-3 cells with 16c caused slight cycle arrest in a concentration-dependent manner. The structure-activity relationships of R¹, R², R³ and linker of the benzimidazole derivatives were analyzed in detail, which would help further exploration of new Pin1 inhibitors.

Gears-In-Motion: The Interplay of WW and PPIase Domains in Pin1

Pin1 belongs to the family of the peptidyl-prolyl cis-trans isomerase (PPIase), which is a class of enzymes that catalyze the cis/trans isomerization of the Proline residue. Pin1 is unique and only catalyzes the phosphorylated Serine/Threonine-Proline (S/T-P) motifs of a subset of proteins. Since the discovery of Pin1 as a key protein in cell cycle regulation, it has been implicated in numerous diseases, ranging from cancer to neurodegenerative diseases. The main features of Pin1 lies in its two main domains: the WW (two conserved tryptophan) domain and the PPIase domain. Despite extensive studies trying to understand the mechanisms of Pin1 functions, how these two domains contribute to the biological roles of Pin1 in cellular signaling requires more investigations. The WW domain of Pin1 is known to have a higher affinity to its substrate than that of the PPIase domain. Yet, the WW domain seems to prefer the trans configuration of phosphorylated S/T-P motif, while the PPIase catalyzes the cis to trans isomerasion. Such contradicting information has generated much confusion as to the actual mechanism of Pin1 function. In addition, dynamic allostery has been suggested to be important for Pin1 function. Henceforth, in this review, we will be looking at the progress made in understanding the function of Pin1, and how these understandings can aid us in overcoming the diseases implicated by Pin1 such as cancer during drug development.

Prolyl isomerase Pin1: a promoter of cancer and a target for therapy

Pin1 is the only known peptidyl-prolyl cis–trans isomerase (PPIase) that specifically recognizes and isomerizes the phosphorylated Serine/Threonine-Proline (pSer/Thr-Pro) motif. The Pin1-mediated structural transformation posttranslationally regulates the biofunctions of multiple proteins. Pin1 is involved in many cellular processes, the aberrance of which lead to both degenerative and neoplastic diseases. Pin1 is highly expressed in the majority of cancers and its deficiency significantly suppresses cancer progression. According to the ground-breaking summaries by Hanahan D and Weinberg RA, the hallmarks of cancer comprise ten biological capabilities. Multiple researches illuminated that Pin1 contributes to these aberrant behaviors of cancer via promoting various cancer-driving pathways. This review summarized the detailed mechanisms of Pin1 in different cancer capabilities and certain Pin1-targeted small-molecule compounds that exhibit anticancer activities, expecting to facilitate anticancer therapies by targeting Pin1.

Design, synthesis and biological evaluation of ring A modified 11-keto-boswellic acid derivatives as Pin1 inhibitors with remarkable anti-prostate cancer activity

Pin1 (Protein interaction with never in mitosis A1) is a validated molecular target for anticancer drug discovery. Herein, we reported the design, synthesis, and structure-activity relationship study of novel ring A modified AKBA (3-acetyl-11-keto-boswellic acid) derivatives as Pin1 inhibitors. Most compounds showed superior Pin1 inhibitory activities to AKBA. One of the most promising compounds, 10a, potently inhibited Pin1 with IC₅₀ value of 0.46 μM, while it displayed excellent anti-proliferative effect against prostate cancer cells PC-3 with GI₅₀ value of 1.82 μM. Structure-activity relationship indicated that reasonable structural modifications in ring A had significant impact on improving activity. Further mechanism research revealed that 10a decreased the level of Cyclin D1 and caused cell cycle arrest at G0/G1 phase in PC-3 cancer cells. Thus, compound 10a may serve as potential anti-prostate cancer agent for further investigation through Pin1 inhibition.