Rational Drug Design Approach Research Articles

Subtractive Proteomics Supported with Rational Drug Design Approach Revealed ZINC23121280 as a Potent Lead Inhibitory Molecule for Multi-drug Resistant Francisella tularensis

Francisella tularensis is a Gram-negative bacterium and is the etiological agent of taluremia. The prolonged use of antibiotics is the reason for pathogen resistance to antibiotics such as beta-lactams and macrolides. This leads to the search to explore novel drug targets for F. tularensis to inhibit its growth. Subtractive proteomics revealed Glucose-1-phosphate thymidylyltransferase (G1PTT) as the most promising protein as a drug target. A pharmacophore model was generated for virtual screening of a druglike library comprised of 1,000,000 drug molecules. Based on a pharmacophore-based search, a set of 152 compounds was predicted as the most potent inhibitors against this enzyme. The screened hits were docked with the target enzyme; which unveiled ZINC23121280 as the best-docked inhibitor having Autdock Vina binding energy of -7.2 kcal/mol and the GOLD score of 64.06. Moreover, the timedependent dynamic behavior of the complex was analyzed using Molecular Dynamics (MD) simulation studies that revealed a stable system with a Root Mean Square Deviation (RMSD) average value of 2.25 Å and Root Mean SquareFluctuations (RMSF) of 1.16 Å. Radial Distribution Function (RDF) predicted strong hydrogen interactions between the ligand and Trp221 from the enzyme active pocket. The higher affinity of the antagonist for the enzyme was further supported by Molecular Mechanics Energies combined with the Poisson–Boltzmann and Surface Area (MMPBSA) and or Generalized Born and Surface Area (MMGBSA) with the estimated binding free energy of −1.07 kcal/mol and −29.59 kcal/mol, respectively. Findings from this present computational framework may provide the foundation for future drug discovery against F. tularensis.

In Vitro and In Vivo Efficacies of the Linear and the Cyclic Version of an All-d-Enantiomeric Peptide Developed for the Treatment of Alzheimer's Disease.

Multiple sources of evidence suggest that soluble amyloid β (Aβ)-oligomers are responsible for the development and progression of Alzheimer’s disease (AD). In order to specifically eliminate these toxic Aβ-oligomers, our group has developed a variety of all-d-peptides over the past years. One of them, RD2, has been intensively studied and showed such convincing in vitro and in vivo properties that it is currently in clinical trials. In order to further optimize the compounds and to elucidate the characteristics of therapeutic d-peptides, several rational drug design approaches have been performed. Two of these d-peptides are the linear tandem (head-to-tail) d-peptide RD2D3 and its cyclized form cRD2D3. Tandemization and cyclization should result in an increased in vitro potency and increase pharmacokinetic properties, especially crossing the blood–brain-barrier. In comparison, cRD2D3 showed a superior pharmacokinetic profile to RD2D3. This fact suggests that higher efficacy can be achieved in vivo at equally administered concentrations. To prove this hypothesis, we first established the in vitro profile of both d-peptides here. Subsequently, we performed an intraperitoneal treatment study. This study failed to provide evidence that cRD2D3 is superior to RD2D3 in vivo as in some tests cRD2D3 failed to show equal or higher efficacy.

Cyclin-Dependent Kinase as a Novel Therapeutic Target: An Endless Story

Cyclin-Dependent Kinases (CDKs) are a family of enzymes that, along with their Cyclin partners, play a crucial role in cell cycle regulation at many biological functions such as proliferation, differentiation, DNA repair, and apoptosis. Thus, they are tightly regulated by a number of inhibitory and activating enzymes. Deregulation of these kinases’ activity either by amplification, overexpression or mutation of CDKs or Cyclins leads to uncontrolled proliferation of cancer cells. Hyperactivity of these kinases has been reported in a wide variety of human cancers. Hence, CDKs have been established as one of the most attractive pharmacological targets in the development of promising anticancer drugs. The elucidated structural features and the well-characterized molecular mechanisms of CDKs have been the guide in designing inhibitors to these kinases. Yet, they remain a challenging therapeutic class as they share conserved structure similarity in their active site. Several inhibitors have been discovered from natural sources or identified through high throughput screening and rational drug design approaches. Most of these inhibitors target the ATP binding pocket, therefore, they suffer from a number of limitations. Here, a growing number of ATP noncompetitive peptides and small molecules has been reported.

Review on Divalent Atom and Group in Bioisosterism

Bioisosterism in rational drug design approach specifically the divalent atom and group in their modification and optimization to improve the pharmacokinetic and pharmacodynamics properties of compound have been studied.

A new synthetic dual agonist of GPR120/GPR40 induces GLP-1 secretion and improves glucose homeostasis in mice

G-protein coupled receptors 40 and 120 (GPR40 and GPR120) are increasingly emerging as potential therapeutic targets for the treatment of altered glucose homeostasis, and their agonists are under evaluation for their glucagon-like peptide-1 (GLP-1)-mediated therapeutic effects on insulin production and sensitivity. Here, we characterized a new dual GPR40 and GPR120 agonist (DFL23916) and demonstrated that it can induce GLP-1 secretion and improve glucose homeostasis.Resulting from a rational drug design approach aimed at identifying new dual GPR120/40 agonists able to delay receptor internalization, DFL23916 had a good activity and a very high selectivity towards human GPR120 (long and short isoforms) and GPR40, as well as towards their mouse orthologous, by which it induced both Gαq/11-initiated signal transduction pathways with subsequent Ca2+ intracellular spikes and G protein-independent signaling via β-arrestin with the same activity. Compared to the endogenous ligand alpha-linolenic acid (ALA), a selective GPR120 agonist (TUG-891) and a well-known dual GPR40 and GPR120 agonist (GW9508), DFL23916 was the most effective in inducing GLP-1 secretion in human and murine enteroendocrine cells, and this could be due to the delayed internalization of the receptor (up to 3 h) that we observed after treatment with DFL23916. With a good pharmacokinetic/ADME profile, DFL23916 significantly increased GLP-1 portal vein levels in healthy mice, demonstrating that it can efficiently induce GLP-1 secretion in vivo. Contrary to the selective GPR120 agonist (TUG-891), DFL23916 significantly improved also glucose homeostasis in mice undergoing an oral glucose tolerance test (OGTT).

The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design.

Tubulin vinca-domain ligands can inhibit microtubule polymerization, causing cell death in mitosis, and their potential against multiple cancer types has been demonstrated. However, due to drug resistance and toxicities, development of novel vinca-domain ligands is still needed. In this study, we determined the high-resolution crystal structures of vinorelbine, YXD, and Phomopsin A in complex with tubulin at 2.5Å. Additionally, we recapitulated all previously published high-resolution crystal structures of the vinca binding site to reveal critical residues and the molecular mechanism of vinca-domain ligands interacting with tubulin. Furthermore, we designed putatively novel triazolopyrimidine derivatives by introducing secondary amine groups to establish salt-bridge and H-bond interactions with Asp179β1 and Asn329α2 . Our studies provided the structural basis for designing novel tubulin vinca-domain ligands.

Discovery of VEGFR-2 inhibitors exerting significant anticancer activity against CD44+ and CD133+ cancer stem cells (CSCs): Reversal of TGF-β induced epithelial-mesenchymal transition (EMT) in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a malignancy characterized by neoangiogenesis, which is an augmented production of proangiogenic factors by the tumor and its adjacent infected cells. These dysregulated angiogenic factors are the therapeutic targets in anti-angiogenic drug development. The signaling pathway of vascular endothelial growth factor (VEGF)/VEGFR-2 is crucial for controlling the angiogenic responses in endothelial cells (ECs). In this study, we carried out a rational drug design approach wherein we have identified the novel orally bioavailable compound VS 8 as a potent VEGFR-2 inhibitor, which remarkably suppresses hVEGF and hVEGFR-2 expression in HUVECs and exhibits significant anti-angiogenic effects in CAM assay. Besides, VS 8 significantly induces apoptosis in HCC cell line (Hep G2). Later we examined its effectiveness against CD44+ and CD133+ CSCs. Here, VS 8 was found to be active against CSCs, and adequate for the cessation of the cell cycle at 'G0/G1' and 'S' phase in CD44+ and CD133+ CSCs respectively. Factually, transforming growth factor-β (TGF-β) stimulated epithelial-mesenchymal transition (EMT) induces invasion and migration of HCC cells, which results in the metastasis. Therefore, we studied the effect of VS 8 on EMT markers using flow cytometry, which suggested that VS 8 significantly upregulates E-cadherin (epithelial biomarker) and downregulates vimentin (mesenchymal biomarker). Further, VS 8 downregulates the expression of EMT-inducing transcription factors (EMT-TFs), i.e., SNAIL. Altogether, our findings indicate that VS 8 could be a promising drug candidate for cancer therapy.

The development of a targeted and more potent, anti-Inflammatory derivative of colchicine: Implications for gout

BackgroundColchicine is routinely used for its anti-inflammatory properties to treat gout and Familial Mediterranean fever. More recently, it was also shown to be of therapeutic benefit for another group of diseases in which inflammation is a key component, namely, cardiovascular disease. Whilst there is considerable interest in repurposing this alkaloid, it has a narrow therapeutic index and is associated with undesirable side effects and drug interactions. We, therefore, developed a derivatives of colchicine that preferentially target leukocytes to increase their potency and diminish their side effects. The anti-inflammatory activity of the colchicine derivatives was tested in experimental models of neutrophil activation by the etiological agent of gout, monosodium urate crystals (MSU). MethodsUsing a rational drug design approach, the structure of colchicine was modified to increase its affinity for βVI-tubulin, a colchicine ligand preferentially expressed by immune cells. The ability of the colchicine analogues with the predicted highest affinity for βVI-tubulin to dampen neutrophil responses to MSU was determined with in vitro assays that measure MSU-induced production of ROS, release of IL-1 and CXCL8/IL-8, and the increase in the concentration of cytoplasmic calcium. The anti-inflammatory property of the derivatives was assessed in the air pouch model of MSU-induced inflammation in mice. ResultsThe most effective compound generated, CCI, is more potent than colchicine in all the in vitro assays. It inhibits neutrophil responses to MSU in vitro at concentrations 10–100-fold lower than colchicine. Similarly, in vivo, CCI inhibits the MSU-induced recruitment of leukocytes at a 10-fold lower concentration than colchicine when administered prior to or after MSU. ConclusionsWe provide evidence that colchicine can be rendered more potent atinhibiting MSU-induced neutrophil activation and inflammation using a rational drug design approach. The development of compounds such as CCI will provide more efficacious drugs that will not only alleviate gout patients of their painful inflammatory episodes at significantly lower doses than colchicine, but also be of potential therapeutic benefit for patients with other diseases treated with colchicine.

Rational Drug Design Approach of Receptor Tyrosine Kinase Type III Inhibitors.

Rational drug design is accomplished through the complementary use of structural biology and computational biology of biological macromolecules involved in disease pathology. Most of the known theoretical approaches for drug design are based on knowledge of the biological targets to which the drug binds. This approach can be used to design drug molecules that restore the balance of the signaling pathway by inhibiting or stimulating biological targets by molecular modeling procedures as well as by molecular dynamics simulations. Type III receptor tyrosine kinase affects most of the fundamental cellular processes including cell cycle, cell migration, cell metabolism, and survival, as well as cell proliferation and differentiation. Many inhibitors of successful rational drug design show that some computational techniques can be combined to achieve synergistic effects.

New Spisulosine Derivative promotes robust autophagic response to cancer cells

Therapy resistance by evasion of apoptosis is one of the hallmarks of human cancer. Therefore, restoration of cell death by non-apoptotic mechanisms is critical to successfully overcome therapy resistance in cancer. By rational drug design approach, here we try to provide evidence that subtle changes in the chemical structure of spisulosine completely switched its cytotoxic function from apoptosis to autophagy. Our most potent molecule (26b) in a series of 16 synthesized derivatives showed robust autophagic cell death in diverse cancer cells sparing normal counterpart. Compound 26b mediated lethal autophagy induction was confirmed by formation of characteristic autophagic vacuoles, LC3 puncta formation, upregulation of signature autophagy markers like Beclin and Atg family proteins. Altogether, we have detected novel autophagy inducer small molecule which can be tested further for drug discovery research.

Metabolism by Aldehyde Oxidase: Drug Design and Complementary Approaches to Challenges in Drug Discovery.

Aldehyde oxidase (AO) catalyzes oxidations of azaheterocycles and aldehydes, amide hydrolysis, and diverse reductions. AO substrates are rare among marketed drugs, and many candidates failed due to poor pharmacokinetics, interspecies differences, and adverse effects. As most issues arise from complex and poorly understood AO biology, an effective solution is to stop or decrease AO metabolism. This perspective focuses on rational drug design approaches to modulate AO-mediated metabolism in drug discovery. AO biological aspects are also covered, as they are complementary to chemical design and important when selecting the experimental system for risk assessment. The authors' recommendation is an early consideration of AO-mediated metabolism supported by computational and in vitro experimental methods but not an automatic avoidance of AO structural flags, many of which are versatile and valuable building blocks. Preferably, consideration of AO-mediated metabolism should be part of the multiparametric drug optimization process, with the goal to improve overall drug-like properties.

Rational drug-design approach supported with thermodynamic studies \u2014 a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2

Numerous inhibitors of protein kinases act on the basis of competition, targeting the ATP binding site. In this work, we present a procedure of rational design of a bi-substrate inhibitor, complemented with biophysical assays. The inhibitors of this type are commonly engineered by combining ligands carrying an ATP-like part with a peptide or peptide-mimicking fragment that determines specificity. Approach presented in this paper led to generation of a specific system for independent screening for efficient ligands and peptides, by means of thermodynamic measurements, that assessed the ability of the identified ligand and peptide to combine into a bi-substrate inhibitor. The catalytic subunit of human protein kinase CK2 was used as the model target. Peptide sequence was optimized using peptide libraries [KGDE]-[DE]-[ST]-[DE]3–4-NH2, originated from the consensus CK2 sequence. We identified KESEEE-NH2 peptide as the most promising one, whose binding affinity is substantially higher than that of the reference RRRDDDSDDD peptide. We assessed its potency to form an efficient bi-substrate inhibitor using tetrabromobenzotriazole (TBBt) as the model ATP-competitive inhibitor. The formation of ternary complex was monitored using Differential Scanning Fluorimetry (DSF), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC).

Abstract 3871: A novel TACC3 inhibitor as an anti-cancer agent in breast cancer

Abstract Transforming Acidic Coiled-Coil Containing Protein 3 (TACC3) is a microtubule-associated protein that is localized on mitotic spindles and ensures proper chromosomal segregation and microtubule stability. TACC3 is frequently amplified or mutated, and was demonstrated to be a prognostic factor in a broad spectrum of cancers which makes it a highly attractive therapeutic target. TACC3 knockdown was demonstrated to cause mitotic spindle defects and prevent proper mitotic progression causing apoptotic cell death. Inhibition of TACC3 with the currently available small molecule inhibitors, KHS101 and SPL-B, has been shown to reduce the growth of glioblastoma xenografts, and suppress tumor growth in ovarian cancer xenografts, respectively. However, none of these TACC3 inhibitors is being tested in clinics potentially due to low systemic stability or high IC50 (inhibitory concentration 50) values. Here, by combining rational drug design and screening approaches, we aimed to identify a novel and more potent TACC3 inhibitor that is effective in in vitro and in vivo systems and that can be used as a mitotic blocker in breast cancer (BC). A library of test compounds was generated by replacing certain functional groups of already available TACC3 inhibitors with their isosteric equivalents to improve potency and drug-like properties. Then, the generated compounds were tested in vitro in terms of growth inhibition in a panel of breast cancer cell lines of different breast cancer subtypes. The compounds were also compared based on their effect on the cellular processes that TACC3 is involved in, and were further compared with genomic TACC3 inhibition by siRNAs. Finally, the most promising agent was tested in vivo in terms of its anti-tumorigenic effects. BO-264 was identified as the most potent TACC3 inhibitor that effectively kills breast cancer cells of different subtypes when administered at nanomolar dose. Moreover, it demonstrated superior inhibitory effects on mitotic progression, DNA repair, and cellular viability as compared to currently available inhibitors. Oral administration of BO-264 suppressed tumor growth in breast cancer xenografts at a dose that caused no apparent toxicity. Specificity of BO-264 to TACC3 protein was tested by kinome profiling and further validated by state-of-art binding assays. Currently, we are testing the pharmacokinetics and pharmacodynamics properties and organ toxicity of our inhibitor and performing the detailed molecular characterization of BO-264-mediated anti-tumor effects. Overall, our preclinical findings suggest that our novel compound (BO-264) is potentially a specific TACC3 inhibitor, causing growth inhibition in breast cancer cell lines and xenograft models by inducing mitotic arrest, DNA damage and apoptosis. Considering the critical importance of TACC3 as a cancer biomarker and driver of disease progression, BO-264 has great potential to be used as a novel therapeutic strategy in BC. Citation Format: Ozge Akbulut, Deniz Lengerli, Ozge Saatci, Elif Duman, Urartu Seker, Burcu Caliskan, Erden Banoglu, Ozgur Sahin. A novel TACC3 inhibitor as an anti-cancer agent in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3871.

SYNTHESIS OF 1,3,4-OXADIAZOLES AS SELECTIVE T-TYPE CALCIUM CHANNEL INHIBITORS.

Neuropathic pain, epilepsy, insomnia, and tremor disorder may arrive from an increase of intracellular Ca2+ concentration through a dysfunction of T-type Ca2+ channels. Thus, T-type calcium channels could be a target in drug discovery for the treatments of neuropathic pain and epilepsy. From rational drug design approach, a group of 2,5-disubstituted 1,3,4-oxadiazole molecules was synthesized and their selective T-type channel inhibitions were evaluated. The synthetic strategy consists of a short sequence of three reactions: (i) condensation of thiosemicarbazide with acid chlorides; (ii) ring closing by 1,3-dibromo-5,5- dimethylhydantoin; and (iii) coupling with various acid chlorides. 5-Chloro-N-(5- phenyl-1,3,4-oxadiazol-2-yl)thiophene-2-carboxamide (11) was found to selectively inhibit T-type Ca2+ channel over Na+ and K+ channels in mouse dorsal root ganglion neurons and/or human embryonic kidney (HEK)-293 cells and to suppress seizure-induced death in mouse model. Consequently, compound 11 is a useful probe for investigation of physiologic and pathophysiologic roles of the T-channel, and provides a basis to develop a novel therapeutic to treat chronic neuropathic and inflammatory pains.

Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions.

Halogen bond interaction between a protein electronegative atom and a ligand halogen atom is increasingly attracting attention in the field of structure-based drug design. Nevertheless, gaps in understanding make it desirable to better examine the role of forces governing the formation of favorable halogen bond interactions, and the development of effective and efficient computational approaches to "design in" favorable halogen bond interactions in lead optimization process are warranted. Here, we analyzed the binding-site water properties of crystal structures with characterized halogen bond interactions between ligand halogen atoms and protein backbone carbonyl groups and, thus, found that halogen atoms involved in halogen bond interactions frequently replace calculated binding-site waters upon ligand binding. Moreover, we observed that the preferential directionality of halogen bond interactions aligns well with the orientations of these replaced waters, and these replaced waters exhibited differential energetic characteristics as compared to waters that are displaced by halogen atoms that do not form halogen bond interactions. Our discovery that replacement of calculated binding-site waters contributes to the formation of favorable halogen bond interactions suggests a practical approach for rational drug design utilizing halogen bond interactions with protein backbone carbonyl groups.

Abstract P2-12-02: discovery of the β-catenin/Tcf inhibitors for treatment of triple negative breast cancer

Abstract In triple negative breast cancers (TNBCs), the autocrine activation of Wnt ligands, the epigenetic silencing of Wnt suppressor genes, and the cross talks between signaling pathways stabilize β-catenin in the dephosphorylated state, increase the level of nuclear β-catenin, and aberrantly activate the Wnt/β-catenin signaling pathway. The design of inhibitors for the upstream effectors of the Wnt/β-catenin signaling pathway cannot confer the inhibitory activities to cancer cells that harbor downstream APC, Axin, or β-catenin activation mutations and can perturb the function of β-catenin in cell–cell adhesion. The formation of the β-catenin/T-cell factor (Tcf) complex in the cell nucleus is the penultimate step of the Wnt/β-catenin signaling pathway. The aberrant formation of this protein–protein interaction (PPI) complex has been recognized as a key driving force for many cancers including TNBCs. Since β-catenin was reported in 1992, significant interest has been paid to screen compound libraries to discover small-molecule inhibitors that can bind β-catenin and disrupt the β-catenin/Tcf interaction. Many high-throughput screening campaigns were conducted, but little to no success was obtained. None of the reported compounds were able to deliver any drug candidates to preclinical and clinical trials. We decided to take a rational drug design approach to design new inhibitors based on the electronic properties of the key structural features for β-catenin/Tcf recognition. Our crystallographic and biochemical analyses revealed that the Tcf4 G13ANDE17 binding site of β-catenin could be targeted to design potent small-molecule inhibitors selective for the β-catenin/Tcf interaction. In combination of peptidomimetic strategy, structure-based drug design, and chemical synthesis, and biochemical and cell-based characterizations, we successfully designed and synthesized potent and selective small-molecule inhibitors for the β-catenin/Tcf interaction. The most potent inhibitor exhibited submicromolar inhibitory potency for disruption of the β-catenin/Tcf interaction. This potent inhibitor also exhibited dozens to hundreds folds of selectivities for the β-catenin/Tcf over the β-catenin/E-cadherin and β-catenin/APC interactions. The binding mode of new inhibitors was characterized by the site-directed mutagenesis and structure-activity relationship studies. The cell-based studies demonstrated that new inhibitors passed the cell membrane, significantly attenuated Wnt/β-catenin signaling in TNBC cells, and suppressed growth of Wnt/β-catenin-dependent TNBC cells. These inhibitors also exhibited cell-based selectivities for the β-catenin/Tcf over β-catenin/cadherin and β-catenin/adenomatous polyposis coli (APC) interactions. Citation Format: Ji H, Wang Z, Mo C, Zhang M. discovery of the β-catenin/Tcf inhibitors for treatment of triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-12-02.

Potent and Broad-Spectrum Antimicrobial Activity of Analogs from the Scorpion Peptide Stigmurin.

Scorpion venom constitutes a rich source of biologically active compounds with high potential for therapeutic and biotechnological applications that can be used as prototypes for the design of new drugs. The aim of this study was to characterize the structural conformation, evaluate the antimicrobial activity, and gain insight into the possible action mechanism underlying it, for two new analog peptides of the scorpion peptide Stigmurin, named StigA25 and StigA31. The amino acid substitutions in the native sequence for lysine residues resulted in peptides with higher positive net charge and hydrophobicity, with an increase in the theoretical helical content. StigA25 and StigA31 showed the capacity to modify their structural conformation according to the environment, and were stable to pH and temperature variation—results similar to the native peptide. Both analog peptides demonstrated broad-spectrum antimicrobial activity in vitro, showing an effect superior to that of the native peptide, being non-hemolytic at the biologically active concentrations. Therefore, this study demonstrates the therapeutic potential of the analog peptides from Stigmurin and the promising approach of rational drug design based on scorpion venom peptide to obtain new anti-infective agents.

From a MMP2/CK2 multitarget approach to the identification of potent and selective MMP13 inhibitors.

In this article, we describe our efforts in the search of MMP2/CK2 dual targeting inhibitors. We have followed a rational drug design approach based on our experience in the selective inhibition of these two enzymes. We have successfully obtained highly active MMP2 (10, IC50 = 70 nM; 11, IC50 = 100 nM) and CK2 (16a, IC50 = 500 nM) inhibitors. However, structural fine tuning of these small molecules to simultaneously target both enzymes turned out to be an unattainable goal. Unexpectedly, we were lucky to identify new and selective MMP13 inhibitors (10, IC50 = 3.7 nM and 11, IC50 = 5.6 nM) with a novel TBB-derived scaffold. These compounds constitute an interesting starting point for further optimization.

Discovery of 4-(((4-(5-chloro-2-(((1s,4s)-4-((2-methoxyethyl)amino)cyclohexyl)amino)pyridin-4-yl)thiazol-2-yl)amino)methyl)tetrahydro-2H-pyran-4-carbonitrile (JSH-150) as a novel highly selective and potent CDK9 kinase inhibitor

Through a structure-guided rational drug design approach, we have discovered a highly selective inhibitor compound 40 (JSH-150), which exhibited an IC50 of 1 nM against CDK9 kinase in the biochemical assay and achieved around 300–10000-fold selectivity over other CDK kinase family members. In addition, it also displayed high selectivity over other 468 kinases/mutants (KINOMEscan S score(1) = 0.01). Compound 40 displayed potent antiproliferative effects against melanoma, neuroblastoma, hepatoma, colon cancer, lung cancer as well as leukemia cell lines. It could dose-dependently inhibit the phosphorylation of RNA Pol II, suppress the expression of MCL-1 and c-Myc, arrest the cell cycle and induce the apoptosis in the leukemia cells. In the MV4-11 cell-inoculated xenograft mouse model, 10 mg/kg dosage of 40 could almost completely suppress the tumor progression. The high selectivity and good in vivo PK/PD profile suggested that 40 would be a good pharmacological tool to study CDK9-mediated physiology and pathology as well as a potential drug candidate for leukemia and other cancers.

From Natural to Artificial Antitumor Lipidic Alkynylcarbinols: Asymmetric Synthesis, Enzymatic Resolution, and Refined SARs

Among acetylenic natural products, chiral lipidic alkynylcarbinol (LAC) metabolites, mostly extracted from marine sponges, have revealed a broad spectrum of biological activities, in particular, remarkable antitumor cytotoxicity. With reference to one of the simplest natural representatives, [(S)-eicos-(4E)-en-1-yn-3-ol], and a given cancer cell line (HCT116), combined extensive efforts in chemical synthesis (relying on the use of a large chemical toolbox) and biological analysis (in vitro tests), have provided systematic structure–activity relationships (SARs) where the initially selected four structural parameters appear as independent principal components: (i) and (ii) the sp/sp2 content and extent of the terminal and internal unsaturations adjacent to the carbinol center, (iii) the absolute configuration of the latter, (iv) the length of the n-aliphatic backbone. Two key criteria have also been established regarding the functional alkynylcarbinol pharmacophore: the alkynylcarbinol unit must be both secondary and terminal (i.e., substituted by a short ethynyl or ethenyl C2 group). This review is intended to provide a further illustration of the value of a simple rational approach for drug design, and to act as a benchmark for future optimization of LACs as antitumor agents.1 Introduction2 2C2-Unsaturated Pharmacophore Candidates2.1 Alkenylalkynylcarbinols (AACs)2.2 Dialkynylcarbinols (DACs or DACys)2.3 Alkynylalkenylcarbinols (iso-AACs) and Dialkenylcarbinols (DACes)2.4 Oxidation-Protected Dialkynylcarbinols and Dialkynylketones2.5 Fluorophore-Labeled Lipidic Dialkynylcarbinols3 C2/C3-Unsaturated Pharmacophore Candidates3.1 Cyclopropylalkynylcarbinols (CACs)3.2 Allenylalkynylcarbinols (AllACs)4 C2/C4- and 3C2-Unsaturated Pharmacophore Candidates4.1 Butadiynylalkynylcarbinols (BACs)4.2 Trialkynylcarbinols (TACs)5 Double-AC-Headed Pharmacophore Candidates6 Screening on the Lipidic Chain Length7 Conclusion