Searching for cyclin-dependent kinase inhibitors using a new variant of the cope elimination

Ring-Opening Sulfonylation of Cyclic Sulfonium Salts with Sodium Sulfinates under Transition-Metal- and Additive-Free Conditions

Incorporating a sulfonyl group into parent molecules has been shown to effectively improve their synthetic applications and bioactivities. In this study, we present a straightforward and practical approach for the ring-opening reaction of alkenyl-aryl sulfonium salts with sodium sulfinates to produce a range of sulfur-containing alkyl sulfones. This method offers the benefits of mild reaction conditions, easily accessible raw materials, wide substrate applicability, good functional group compatibility, and operational simplicity. Importantly, the resulting products can be readily converted into sulfoxides, sulfones, sulfoximines, and some heterocyclic compounds.

Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase

Reverse transcriptase (RT) is one of three key proteins responsible for the replication cycle of HIV-1 in the host. Several classes of inhibitors have been developed to target the enzyme, with non-nucleoside reverse transcriptase inhibitors forming first-line treatment. Previously, covalent RT inhibitors have been identified and found to bind irreversibly to commonly mutated residues such as Y181C. In this work we aim to circumvent the issue of NNRTI resistance through targeting K102, which has not yet been identified to confer drug resistance. As reported here, 34 compounds were synthesized and characterized biochemically and structurally with wild-type (WT) HIV-1 RT. Two of these inhibitors demonstrate covalent inhibition as evidenced by protein crystallography, enzyme kinetics, mass spectrometry, and antiviral potency in HIV-1 infected human T-cell assays.

Fluorescence Imaging of Intracellular Glutathione Levels in the Endoplasmic Reticulum to Reveal the Inhibition Effect of Rutin on Ferroptosis

Ferroptosis is an emerging form of nonapoptotic cell death, and the search for novel ferroptosis inhibitors is of great importance to explore unique cytoprotective strategies against ferroptosis-relevant diseases. In this work, we present an endoplasmic reticulum-targeting fluorescent probe (ER-G) for the imaging of intracellular glutathione (GSH) levels and revealed the inhibition effect of rutin on ferroptosis. Structurally, ER-G utilized a cyclohexyl sulfonylurea as the endoplasmic reticulum-targeting unit, and single-crystal X-ray diffraction analysis confirmed that ER-G possessed a N-oxide pyridine sulfinyl group instead of sulfone. After the response of ER-G to GSH, the fluorescence intensity at 523 nm displayed a significant increase by 3900-fold. ER-G showed extreme sensitivity and selectivity to GSH. The fluorescence imaging results demonstrated that ER-G exhibited excellent endoplasmic reticulum-targeting properties and could be applied to monitor GSH levels in the endoplasmic reticulum during the erastin-induced ferroptosis process. By the fluorescence imaging of GSH levels in the endoplasmic reticulum, it was demonstrated that rutin could efficiently block the depletion of GSH during erastin-induced ferroptosis and potentially act as a novel ferroptosis inhibitor. Moreover, unlike traditional ferroptosis inhibitors, it was speculated that the inhibition mechanism of rutin to ferroptosis was the integration of the chelate effect on Fe(II) ions and antioxidant effect. We expect that fluorescence imaging of GSH levels in the endoplasmic reticulum could provide a convenient and feasible method to evaluate the inhibition effect of small molecules on ferroptosis.

A sustainable photochemical aerobic sulfide oxidation: access to sulforaphane and modafinil

Sulfoxide-containing molecules are an important class of compounds in the pharmaceutical industry and many efforts have been made to develop new and green protocols, targeting the chemoselective transformation of sulfides into sulfoxides. Photochemistry is a rapidly expanding research field employing light as the energy source. Photochemical aerobic processes possess additional advantages to photochemistry and may find applications in the chemical industries. Herein, a 370 nm catalyst-free aerobic protocol was developed, using 2-Me-THF as the green solvent. At the same time, two low-catalyst-loading anthraquinone-based processes (under a CFL lamp or 427 nm irradiation) in 2-Me-THF were developed. Furthermore, a broad range of substrates was tested. We also implemented our protocols towards the synthesis of the pharmaceutical active ingredients (APIs) sulforaphane and modafinil.

Chemoselective O-Alkylation of 4-(Trifluoromethyl)pyrimidin-2(1H)-ones Using 4-(Iodomethyl)pyrimidines

This study reports two strategies for preparing O-alkyl derivatives of 6-substituted-4-(trifluoromethyl)pyrimidin-(1H)-ones: a linear protocol of alkylation, using a CCC-building block followed by [3 + 3]-type cyclocondensation with 2-methylisothiourea sulfate and a convergent protocol based on direct alkylation, using 4-(iodomethyl)-2-(methylthio)-6-(trihalomethyl)pyrimidines. It was found that the cyclocondensation strategy is not feasible; thus, the direct chemoselective O-alkylation was performed, and 18 derivatives of the targeted pyrimidines were obtained in 70-98% yields. The structure of the products was unambiguously determined via single crystal X-ray analyses and two-dimensional nuclear magnetic resonance experiments.

Cerium-Oxo clusters for photocatalytic aerobic oxygenation of sulfides to sulfoxides

Two cerium-oxo clusters (COCs) 1 and 2 are constructed by self-assembly of cerium ions and carboxylate ligands. Both clusters feature spherical structures resembling the key moiety of fluorite phase CeO2,...

A revised synthesis of 6-alkoxy-2-aminopurines with late-stage convergence allowing for increased molecular complexity

This streamlined synthesis allows the alcohol at the 6-position of 6-alkoxy-2-arylaminopurines to be used only in moderate excess, rather than as solvent, opening up the possibility of accessing more complicated molecules.

Serendipitous synthesis of 2-alkenyl- and 2-aryl-4-thiazolidinones using dithiodiglycolic anhydride

Dithiodiglycolic anhydride undergoes an efficient formal cycloaddition with imines to afford functionalized 4-thiazolidinones, without complications arising from the anhydride-imine reaction or the sulfa-Michael reaction (in the case of 1,3-azadienes).

Selective synthesis of sulfoxides and sulfones via controllable oxidation of sulfides with N-fluorobenzenesulfonimide

A practical and mild method for the switchable synthesis of sulfoxides or sulfones via selective oxidation of sulfides using cheap N-fluorobenzenesulfonimide (NFSI) as the oxidant has been developed. These highly chemoselective transformations were simply achieved by varying the NFSI loading with H₂O as the green solvent and oxygen source without any additives. The good functional group tolerance makes the strategy valuable.

A three-component reaction of arynes, sodium sulfinates, and aldehydes toward 2-sulfonyl benzyl alcohol derivatives

A novel three-component reaction of arynes, sodium sulfinates, and aldehydes under mild reaction conditions is described. This transformation provides a direct synthetic approach to 2-sulfonyl benzyl alcohol derivatives, which could be rapidly converted to diverse arylsulfur compounds via the transformation of the corresponding hydroxyl groups. Various aryne precursors, sodium arenesulfinates, and aromatic aldehydes can be effectively converted to the desired products in 40-84% yields (29 examples).

Metal-free sulfonylative annulations of alkyl diiodides with sulfur dioxide: synthesis of cyclic aliphatic sulfones

A straightforward protocol for cyclic aliphatic sulfones is effectively established via sulfonylative annulations of alkyl diiodides and gaseous sulfur dioxide. Five- to nine-membered cyclic aliphatic sulfones were afforded in this manner.

2-Arylamino-6-ethynylpurines are cysteine-targeting irreversible inhibitors of Nek2 kinase

Renewed interest in covalent inhibitors of enzymes implicated in disease states has afforded several agents targeted at protein kinases of relevance to cancers. We now report the design, synthesis and biological evaluation of 6-ethynylpurines that act as covalent inhibitors of Nek2 by capturing a cysteine residue (Cys22) close to the catalytic domain of this protein kinase. Examination of the crystal structure of the non-covalent inhibitor 3-((6-cyclohexylmethoxy-7H-purin-2-yl)amino)benzamide in complex with Nek2 indicated that replacing the alkoxy with an ethynyl group places the terminus of the alkyne close to Cys22 and in a position compatible with the stereoelectronic requirements of a Michael addition. A series of 6-ethynylpurines was prepared and a structure activity relationship (SAR) established for inhibition of Nek2. 6-Ethynyl-N-phenyl-7H-purin-2-amine [IC50 0.15 μM (Nek2)] and 4-((6-ethynyl-7H-purin-2-yl)amino)benzenesulfonamide (IC50 0.14 μM) were selected for determination of the mode of inhibition of Nek2, which was shown to be time-dependent, not reversed by addition of ATP and negated by site directed mutagenesis of Cys22 to alanine. Replacement of the ethynyl group by ethyl or cyano abrogated activity. Variation of substituents on the N-phenyl moiety for 6-ethynylpurines gave further SAR data for Nek2 inhibition. The data showed little correlation of activity with the nature of the substituent, indicating that after sufficient initial competitive binding to Nek2 subsequent covalent modification of Cys22 occurs in all cases. A typical activity profile was that for 2-(3-((6-ethynyl-9H-purin-2-yl)amino)phenyl)acetamide [IC50 0.06 μM (Nek2); GI50 (SKBR3) 2.2 μM] which exhibited >5-10-fold selectivity for Nek2 over other kinases; it also showed > 50% growth inhibition at 10 μM concentration against selected breast and leukaemia cell lines. X-ray crystallographic analysis confirmed that binding of the compound to the Nek2 ATP-binding site resulted in covalent modification of Cys22. Further studies confirmed that 2-(3-((6-ethynyl-9H-purin-2-yl)amino)phenyl)acetamide has the attributes of a drug-like compound with good aqueous solubility, no inhibition of hERG at 25 μM and a good stability profile in human liver microsomes. It is concluded that 6-ethynylpurines are promising agents for cancer treatment by virtue of their selective inhibition of Nek2.

Sulfoxidation inside a hypercrosslinked microporous network nanotube catalyst

In the present work, a kind of efficient heterogeneous catalyst was synthesized from amine-functionalized hypercrosslinked bottlebrush copolymers of microporous network nanotubes (amine-MNNs) and Na₂WO₄.

Cobalt Single-Atom-Intercalated Molybdenum Disulfide for Sulfide Oxidation with Exceptional Chemoselectivity

The identification of chemoselective oxidation process en route to fine chemicals and specialty chemicals is a long-standing pursuit in chemical synthesis. A vertically structured, cobalt single atom-intercalated molybdenum disulfide catalyst (Co₁ -in-MoS₂ ) is developed for the chemoselective transformation of sulfides to sulfone derivatives. The single-atom encapsulation alters the electron structure of catalyst owing to confinement effect and strong metal-substrate interaction, thus enhancing adsorption of sulfides and chemoselective oxidation at the edge sites of MoS₂ to achieve excellent yields of up to 99% for 34 examples. The synthetic scopes can be extended to sulfide-bearing alkenes, alkynes, aldehydes, ketones, boronic esters, and amines derivatives as a toolbox for the synthesis of high-value, multifunctional sulfones and late-stage functionalization of pharmaceuticals, e.g., Tamiflu. The synthetic utility of cobalt single atom-intercalated MoS₂ , together with its reusability, scalability, and simplified purification process, renders it promising for industrial productions.

Synthesis and nano-Pd catalyzed chemoselective oxidation of symmetrical and unsymmetrical sulfides

A highly chemoselective, efficient and nano-Pd catalyzed protocol for the rapid construction of sulfoxides and sulfones via the oxidation of symmetrical and unsymmetrical sulfides using H2O2 as an oxidant has been developed, respectively. The ready availability of starting materials, easy recovery and reutilization of the catalyst, wide substrate scope, and high yields make this protocol an attractive alternative. The process also involves the metal-free and microwave-promoted synthesis of symmetrical diarylsulfides, and FeCl3-mediated preparation of symmetrical diaryldisulfides through the reaction of arenediazonium tetrafluoroborates with Na2S·9H2O as a sulfur source. In addition, unsymmetrical sulfides were generated via the K2CO3-mediated reaction of arenediazonium tetrafluoroborates with symmetrical disulfides.

Recent development of CDK inhibitors: An overview of CDK/inhibitor co-crystal structures

The cyclin-dependent protein kinases (CDKs) are protein-serine/threonine kinases that display crucial effects in regulation of cell cycle and transcription. While the excessive expression of CDKs is intimate related to the development of diseases including cancers, which provides opportunities for disease treatment. A large number of small molecules are explored targeting CDKs. CDK/inhibitor co-crystal structures play an important role during the exploration of inhibitors. So far nine kinds of CDK/inhibitor co-crystals have been determined, they account for the highest proportion among the Protein Data Bank (PDB) deposited crystal structures. Herein, we review main co-crystals of CDKs in complex with corresponding inhibitors reported in recent years, focusing our attention on the binding models and the pharmacological activities of inhibitors.

An unprecedented N- to C-sulfonyl migration in the reaction of azomethine amine and allenoates: access to arylsulfonylmethyl substituted pyrazolo[1,5-c]quinazoline and mechanistic studies

A serendipitous discovery of [1,3]-sulfonyl migration has been made in the two-component reaction of azomethine imine and allenoates.

Sodium sulfate–hydrogen peroxide–sodium chloride adduct: selective protocol for the oxidative bromination, iodination and temperature dependent oxidation of sulfides to sulfoxides and sulfones

Sodium sulfate–hydrogen peroxide–sodium chloride adduct: selective protocols for anilines and sulfides oxidation.

A one-pot metal-free protocol for the synthesis of chalcogenated furans from 1,4-enediones and thiols

Transition-metal-free synthesis of chalcogenated furans through the sequential thiol-Michael/Paal–Knorr reaction of 1,4-enediones in the presence of a catalytic amount of p-toluene sulfonic acid has been developed.

Schiff base complex conjugates of bovine serum albumin as artificial metalloenzymes for eco-friendly enantioselective sulfoxidation

Artificial metalloenzymes (BSA-ML) have been prepared by non-covalent insertion of transition metal Schiff-base complexes, ML (L = 2-hydroxynaphthalen-1-naphthaldehyde and 3,4-diaminobenzenesulfonic acid; M = Co, Mn, V, Fe, Cr), into bovine serum albumin (BSA) as the host protein and were characterized by UV-visible spectroscopy, ESI-TOF mass spectrometry and molecular docking studies. The catalytic activities of the BSA-ML in the selective oxidation of various prochiral sulfides in aqueous media, using H2O2 as oxidant, have been evaluated. During the optimization process, pH and the concentrations of catalyst and oxidant were found to have a remarkable influence on both yield and enantioselectivity. In certain cases, BSA-ML gave satisfactory results in the oxidation of organic sulfides to sulfoxides (up to 100% conversion, 100% chemoselectivity, 96% ee and 500 h-1 turnover frequency).

Cross-Coupling of Sodium Sulfinates with Aryl, Heteroaryl, and Vinyl Halides by Nickel/Photoredox Dual Catalysis

An efficient photoredox/nickel catalyzed sulfonylation reaction of aryl, heteroaryl, and vinyl halides has been achieved for the first time. This newly developed sulfonylation protocol provides a versatile method for the synthesis of diverse aromatic sulfones at room temperature and shows excellent functional group tolerance. The electrophilic coupling partners are not limited to aryl, heteroaryl, and vinyl bromides and iodides, but also includes less reactive aryl chlorides as suitable substrates for this transformation.

Efficient and selective oxidation of sulfides in batch and continuous flow using styrene-based polymer immobilised ionic liquid phase supported peroxotungstates

Good conversion and high selectivity for sulfoxidation have been achieved under segmented and continuous flow using a polystyrene-based polymer immobilised ionic liquid phase (PIILP) peroxotungstate.

Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods

Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.

Identification and Characterization of an Irreversible Inhibitor of CDK2

Irreversible inhibitors that modify cysteine or lysine residues within a protein kinase ATP binding site offer, through their distinctive mode of action, an alternative to ATP-competitive agents. 4-((6-(Cyclohexylmethoxy)-9H-purin-2-yl)amino)benzenesulfonamide (NU6102) is a potent and selective ATP-competitive inhibitor of CDK2 in which the sulfonamide moiety is positioned close to a pair of lysine residues. Guided by the CDK2/NU6102 structure, we designed 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300), which binds covalently to CDK2 as shown by a co-complex crystal structure. Acute incubation with NU6300 produced a durable inhibition of Rb phosphorylation in SKUT-1B cells, consistent with it acting as an irreversible CDK2 inhibitor. NU6300 is the first covalent CDK2 inhibitor to be described, and illustrates the potential of vinyl sulfones for the design of more potent and selective compounds.

Insights into the structural basis of 3,5-diaminoindazoles as CDK2 inhibitors: prediction of binding modes and potency by QM-MM interaction, MESP and MD simulation

The novel 3,5-diaminoindazole derivatives are well-known as potent and anti-proliferative cyclin-dependent kinase 2 inhibitors. We report a combined quantum mechanics/molecular mechanics study to determine the protein-ligand interaction energy, and some quantum chemical descriptors to successfully rank these inhibitors. The results in this work show that the QM-MM interaction energy is strongly correlated to the biological activity and can be used as a predictor, which was further validated by Spearman's rank correlation coefficient. An exhaustive analysis of the protein-ligand structures obtained from molecular dynamics simulations shows specific interactions within the active site. Furthermore, the docking study was supported by electronic property analysis using density functional theory at the B3LYP/3-21*G level. The results obtained from molecular docking and surface analysis shed some insight on steric and electronic complementarities of these molecules to CDK2. Aqueous solvation energy values give an indication of the solubility and can be used as a guide for the pharmacokinetic optimization of these molecules. Furthermore, ADME/T properties calculated are in the desirable range, so these compounds are predicted to be drug like with low toxicity potential. Overall, the approach was successful in the cases considered, and it could be useful for the design of inhibitors in the lead optimization phase of drug discovery against CDK2.

Selective remote C–H sulfonylation of aminoquinolines with arylsulfonyl chlorides via copper catalysis

Copper-catalysed remote C−H bond sulfonylation of aminoquinolines using commercially available and inexpensive arylsulfonyl chlorides as the sulfonylation reagents is described.

Comparative analysis of various electrostatic potentials on docking precision against cyclin-dependent kinase 2 protein: a multiple docking approach

The fundamental of molecular modeling is the interaction and binding to form a complex, because it explains the action of most drugs to a receptor active site. In the present study, different semiempirical (RM1, AM1, PM3, MNDO) and ab initio (HF, DFT) charge models were investigated for their performance in prediction of docking pose against CDK2 proteins with their respective inhibitor. Further, multiple docking approaches and Prime/MM-GBSA calculations were applied to predict the binding mode with respective charge model against CDK2 inhibitors. A reliable docking result was obtained using RRD, which showed significance improvement on ligand binding poses and docking score accuracy to the IFD. The combined use of RRD and Prime/MM-GBSA method could give a high correlation between the predicted binding free energy and experimental biological activity. The preliminary results point out that AM1 could be a precious charge model for design of new drugs with enhanced success rate. As a very similar result was also found for a different system of the protein-ligand binding, the suggested scoring function based on AM1 method seems to be applicable in drug design. The results from this study can provide insights into highest success rate for design of potent and selective CDK2 inhibitors.

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein-ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O-O radial distribution functions similar to TIP4P-EW.

meta-Chloroperbenzoic acid (mCPBA): a versatile reagent in organic synthesis

This review aims to collect and discuss the synthetic applications of meta-chloroperbenzoic acid (mCPBA) over the past few decades.

A structure-guided approach for protein pocket modeling and affinity prediction

Binding affinity prediction is frequently addressed using computational models constructed solely with molecular structure and activity data. We present a hybrid structure-guided strategy that combines molecular similarity, docking, and multiple-instance learning such that information from protein structures can be used to inform models of structure-activity relationships. The Surflex-QMOD approach has been shown to produce accurate predictions of binding affinity by constructing an interpretable physical model of a binding site with no experimental binding site structural information. We introduce a method to integrate protein structure information into the model induction process in order to construct more robust physical models. The structure-guided models accurately predict binding affinities over a broad range of compounds while producing more accurate representations of the protein pockets and ligand binding modes. Structure-guidance for the QMOD method yielded significant performance improvements, both for affinity and pose prediction, especially in cases where predictions were made on ligands very different from those used for model induction.

Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors

Molecular docking, free energy calculation and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 3,5-diaminoindazoles, imidazo(1,2-b)pyridazines and triazolo(1,5-a) pyridazines series of Cyclin-dependent kinase (CDK2) inhibitors. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviations (RMSDs). We found different binding sites namely catalytic, inhibitory phosphorylation, cyclin binding and CKS-binding site of the CDK2 contributing towards the binding of these compounds. Moreover, correlation between free energy of binding and biological activity yielded a statistically significant correlation coefficient. Finally, three representative protein-ligand complexes were subjected to molecular dynamics simulation to determine the stability of the predicted conformations. The low value of the RMSDs between the initial complex structure and the energy minimized final average complex structure suggests that the derived docked complexes are close to equilibrium. We suggest that the phenylacetyl type of substituents and cyclohexyl moiety make the favorable interactions with a number of residues in the active site, and show better inhibitory activity to improve the pharmacokinetic profile of compounds against CDK2. The structure-based drug design strategy described in this study will be highly useful for the development of new inhibitors with high potency and selectivity.

Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery

Fragment-based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high-affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency.

Computational study of the interactions between guanine derivatives and cyclin-dependent kinase 2 (CDK2) by CoMFA and QM/MM

Comparative molecular field analysis (CoMFA) and QM/MM hybrid calculations were performed on 9H-purine derivatives as CDK2 inhibitors. CoMFA was carried out to describe the activities of 78 analogues. The models were applied to a training set including 64 compounds. The best CoMFA model included steric and electrostatic fields, had a good Q(2) value of 0.845, and adequately predicted the compounds contained in the test set. Furthermore, plots of the steric CoMFA field allowed conclusions to be drawn for the choice of suitable inhibitors. In addition, the dynamical behavior of compounds with 4-(aminosulfonyl)phenyl, 4-[(methylamino)sulfonyl]phenyl, 4-[(dimethylamino)sulfonyl]phenyl, and [3-methoxy-4-(aminosulfonyl)]phenyl groups at position 2 of the 9H-purine scaffold inside the CDK2 active site were analyzed by QM/MM calculations. The interactions of these compounds with residues Lys89, Asp86, and Ile10 were characterized.

Improved procedure for the synthesis of enamine N-oxides

An improved procedure for the preparation of enamine N-oxides involving aminolysis of epoxides, chlorination, N-oxidation, and dehydrochlorination is described. Although isolated beta-chloroamine N-oxides are prone to rearrangements when isolated, these side reactions can be slowed by the presence of stabilizing organic acids. The scope and limitations of this strategy are discussed.