Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking

Serine/Threonine Protein Kinases as Attractive Targets for Anti-Cancer Drugs-An Innovative Approach to Ligand Tuning Using Combined Quantum Chemical Calculations, Molecular Docking, Molecular Dynamic Simulations, and Network-like Similarity Graphs

Serine/threonine protein kinases (CK2, PIM-1, RIO1) are constitutively active, highly conserved, pleiotropic, and multifunctional kinases, which control several signaling pathways and regulate many cellular functions, such as cell activity, survival, proliferation, and apoptosis. Over the past decades, they have gained increasing attention as potential therapeutic targets, ranging from various cancers and neurological, inflammation, and autoimmune disorders to viral diseases, including COVID-19. Despite the accumulation of a vast amount of experimental data, there is still no "recipe" that would facilitate the search for new effective kinase inhibitors. The aim of our study was to develop an effective screening method that would be useful for this purpose. A combination of Density Functional Theory calculations and molecular docking, supplemented with newly developed quantitative methods for the comparison of the binding modes, provided deep insight into the set of desirable properties responsible for their inhibition. The mathematical metrics helped assess the distance between the binding modes, while heatmaps revealed the locations in the ligand that should be modified according to binding site requirements. The Structure-Binding Affinity Index and Structural-Binding Affinity Landscape proposed in this paper helped to measure the extent to which binding affinity is gained or lost in response to a relatively small change in the ligand's structure. The combination of the physico-chemical profile with the aforementioned factors enabled the identification of both "dead" and "promising" search directions. Tests carried out on experimental data have validated and demonstrated the high efficiency of the proposed innovative approach. Our method for quantifying differences between the ligands and their binding capabilities holds promise for guiding future research on new anti-cancer agents.

TMSOTf-Catalyzed Reactions of N-Arylynamides with Sulfilimines To Construct 2-Aminoindoles and α-Arylated Amidines

Here, we disclose an efficient TMSOTf-catalyzed C-H annulation of aryl-terminated N-arylynamides with sulfilimines, leading to the practical assembly of various valuable 2-aminoindoles in generally moderate to excellent yields with a broad range of functional groups, while nonaryl terminated N-arylynamides undergo TMSOTf-catalyzed aminative arylation with sulfilimines providing α-arylated amidines.

Synthesis of Luminescent Indolo[2,1-b]quinazolin-6(12H)-ones via a Sequential Ugi/Iodine-Promoted Cyclization/Staudinger/Aza-Wittig Reaction

A new efficient synthesis of indolo[2,1-b]quinazolin-6(12H)-ones via a sequential Ugi/iodine-promoted cyclization/Staudinger/aza-Wittig reaction was developed. The acid catalyzed three-component reactions of 2-azidobenzaldehydes, 2-[2-(trimethylsilyl)ethynyl]benzenamines (or o-aminoacetophenones), and isocyanides gave Ugi-3CR intermediates, which reacted subsequently with I2/DMSO and triphenylphosphine to produce indolo[2,1-b]quinazolin-6(12H)-ones in good overall yields. The obtained indolo[2,1-b]quinazolin-6(12H)-ones were all colored in bright red or orange. Their luminescent property was studied preliminarily and some of them showed high molar absorption coefficients, strong fluorescence emission intensity, and good absolute light quantum yields.

Easy Access to Phenanthridinones via Metal-Free Cascade Benzannulation and C-N Bond Formation

A concise route for the synthesis of dihydrobenzo[j]phenanthridinones has been disclosed through an aryne annulation strategy under metal-free reaction conditions. The reaction involves multiple C-C and C-N bond cleavages/formations via Diels-Alder reaction, aromatization-driven C-N bond cleavage, and amide formation.

Recyclable gold(I)-catalyzed heterocyclization of ynamides with benzyl or indolyl azides towards 2-aminoindoles or 3-amino-β-carbolines

A highly efficient heterogeneous gold(I)-catalyzed heterocyclization of ynamides with benzyl or indolyl azides has been achieved in 1,2-dichloroethane under mild conditions via a heterogenized α-imino gold carbene intermediate using 5 mol% of SBA-15-anchored strongly hindered NHC-gold(I) complex [IPr-SBA-15-AuNTf2] as the catalyst, delivering a wide range of valuable 2-aminoindoles or 3-amino-β-carbolines in mostly good to excellent yields with high regioselectivity. Furthermore, the new heterogenized NHC-gold(I) complex displays the same catalytic activity as IPrAuNTf2 and is facile to recover by centrifugation of the reaction mixture and can be reused at least seven times without any appreciable drop in its catalytic activity.

Structure-guided discovery of adenosine triphosphate-competitive casein kinase 2 inhibitors

Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic serine-threonine kinase. CK2 has been identified as a potential drug target for the treatment of cancer and related disorders. Several adenosine triphosphate-competitive CK2 inhibitors have been identified and have progressed at different levels of clinical trials. This review presents details of CK2 protein, structural insights into adenosine triphosphate binding pocket, current clinical trial candidates and their analogues. Further, it includes the emerging structure-based drug design approaches, chemistry, structure-activity relationship and biological screening of potent and selective CK2 inhibitors. The authors tabulated the details of CK2 co-crystal structures because these co-crystal structures facilitated the structure-guided discovery of CK2 inhibitors. The narrow hinge pocket compared with related kinases provides useful insights into the discovery of CK2 inhibitors.

Design of 2-amino-6-methyl-pyrimidine benzoic acids as ATP competitive casein kinase-2 (CK2) inhibitors using structure- and fragment-based design, docking and molecular dynamic simulation studies

Overexpression of casein kinase-2 (CK2) has been implicated in several carcinomas, mainly lung, prostate and acute myeloid leukaemia. The smaller nucleotide pocket compared to related kinases provides a great opportunity to discover newer ATP-competitive CK2 inhibitors. In this study, we have employed an integrated structure- and fragment-based design strategy to design 2-amino-6-methyl-pyrimidine benzoic acids as ATP-competitive CK2 inhibitors. A statistically significant four features-based E-pharmacophore (ARRR) model was used to screen 780,092 molecules. Further, the retrieved hits were considered for molecular docking study to identify essential binding interactions. At the same time, fragment-based virtual screening was performed using a dataset of 1,542,397 fragments. The identified hits and fragments were used as structure templates to rationalize the design of 2-amino-6-methyl-pyrimidine benzoic acids as newer CK2 inhibitors. Finally, the binding interactions of the designed hits were identified using an induced fit docking (IFD) study, and their stability was estimated by a molecular dynamics (MD) simulation study of 100 ns.

Strategies of Targeting CK2 in Drug Discovery: Challenges, Opportunities, and Emerging Prospects

CK2 (casein kinase 2) is a serine/threonine protein kinase that is ubiquitous in eukaryotic cells and plays important roles in a variety of cellular functions, including cell growth, apoptosis, circadian rhythms, DNA damage repair, transcription, and translation. CK2 is involved in cancer pathogenesis and the occurrence of many diseases. Therefore, targeting CK2 is a promising therapeutic strategy. Although many CK2-specific small-molecule inhibitors have been developed, only CX-4945 has progressed to clinical trials. In recent years, novel CK2 inhibitors have gradually become a research hotspot, which is expected to overcome the limitations of traditional inhibitors. Herein, we summarize the structure, biological functions, and disease relevance of CK2 and emphatically analyze the structure-activity relationship (SAR) and binding modes of small-molecule CK2 inhibitors. We also discuss the latest progress of novel strategies, providing insights into new drugs targeting CK2 for clinical practice.

Cu-Catalyzed decarboxylative annulation of N-substituted glycines with 3-formylchromones: synthesis of functionalized chromeno[2,3-b]pyrrol-4(1H)-ones

A novel protocol was developed for preparing functionalized chromeno[2,3-b]pyrrol-4(1H)-ones 3 (CMPOs) from 3-formylchromones with N-substituted glycine derivatives. The method entailed decarboxylative annulation of the acyl group of 3-formylchromones by simply heating a mixture of substrates 1-2 and toluene oxidized by 2-di-tert-butyl peroxide (DTBP) and catalyzed by CuBr. As a result, a series of CMPOs 3 were produced via a cascade reaction. This protocol can be used to synthesize functionalized CMPOs via combinatorial and parallel syntheses in a one-pot reaction rather than a tedious multi-step reaction.

A synthesis of fuctionalized 2-amino-3-cyano pyrroles from terminal alkynes, sulfonyl azides and phenacylmalononitriles

A new strategy for the construction of functionalized 2-amino-3-cyano pyrroles has been developed. The reactions involved a copper-catalyzed azide-alkyne cycloaddtion reaction between terminal alkynes and sulfonyl azides followed by generation of N-sulfonoketenimine intermediates. Interception of these reactive ketenimines by phenacylmalononitriles in the presence of copper(I) iodide and Et₃N afforded the expected products. The reaction proceeded smoothly in THF at ambient temperature to afford the target compounds in 70-92% yields and excellent regioselectivity. Evidence for the structure of a typical product is obtained from single-crystal X-ray analyses.

Copper-catalyzed N-arylation of indoles

Abstract:

Over the past decades, the N-arylation of indoles has gained an inevitable role in the fields of material science, pharmaceuticals, and agrochemical industries. They are the basic core skeleton of many natural products. Their synthesis by Ullmann-type C–N coupling reaction of indole derivatives with aryl halides through various catalytic protocols is well explored. Transition metal catalysis was the best method for synthesizing 1-aryl indoles, and copper catalysis is the leading among them. This review comprehends the recent developments in the copper-catalyzed C–N cross-coupling of indoles with aryl halides from 2010 to 2022.

Synthesis and in vitro evaluation of antitumor activity of spiro[indolo[2,1-b]quinazoline-pyrano[2,3-d]pyrimidine] and spiro[indolo[2,1-b]quinazoline-pyrido[2,3-d]pyrimidine] derivatives by using 2D and 3D cell culture models

Cancer as one of the biggest human health problems remains unsolved. The identification of novel platforms with the highest efficacy and low toxicity is a big challenge among interested researchers. In this regard, we are interested to synthesis and evaluate antitumor activity of spiro[indolo[2,1-b]quinazoline-pyrano[2,3-d]pyrimidine] and spiro[indolo[2,1-b]quinazoline-pyrido[2,3-d]pyrimidine] derivatives. The spiro heterocycles were synthesized via four-component reaction of isatoic anhydride, isatins, malononitrile, and some CH-acids including barbituric acid/thiobarbituric acid and 4(6)-aminouracil in CH₂Cl₂ under reflux condition. The significant features of this process are short reaction time, easy purification without chromatographic process, and high yields which make it attractive. Next, we employed 2D and 3D cell culture models to evaluate biological activity of our compounds. Our results showed that among our seven products (4a-g), the compounds 4a and 4e are the best with 50% growth inhibitory concentration (IC₅₀) value lower than etoposide. Our results support this idea that the compounds 4a and 4e may be potential for drug designing in cancer therapy. However, more experiments will be required to find possible side effects of related compounds in vivo.

Downfalls of Chemical Probes Acting at the Kinase ATP-Site: CK2 as a Case Study

Protein kinases are a large class of enzymes with numerous biological roles and many have been implicated in a vast array of diseases, including cancer and the novel coronavirus infection COVID-19. Thus, the development of chemical probes to selectively target each kinase is of great interest. Inhibition of protein kinases with ATP-competitive inhibitors has historically been the most widely used method. However, due to the highly conserved structures of ATP-sites, the identification of truly selective chemical probes is challenging. In this review, we use the Ser/Thr kinase CK2 as an example to highlight the historical challenges in effective and selective chemical probe development, alongside recent advances in the field and alternative strategies aiming to overcome these problems. The methods utilised for CK2 can be applied to an array of protein kinases to aid in the discovery of chemical probes to further understand each kinase's biology, with wide-reaching implications for drug development.

An Environmentally Benign Cascade Reaction of 1,1-Enediamines (EDAMs) for Site-Selective Synthesis of Highly Functionalized 2,10-Dihydro-1H-imidazo[1',2':1,6]pyrido[2,3-b]indoles and Pyrroles

A novel protocol for the synthesis of pyrido[2,3-b]indoles (α-carbolines, 3) from (E)-3-(2-oxo-2-phenylethylidene) indolin-2-one derivatives 1 and 1,1-enediamine (EDAM) 2a via an unexpected cascade reaction in ethanol was developed. Pyrido[2,3-b]indole derivatives 4 were obtained by the same reaction, albeit by stirring the mixture for a longer period of time (about 48 h). As a result, two kinds of functionalized α-carbolines 3 and 4 were synthesized by the facile reaction of the (E)-3-(2-oxo-2-phenylethylidene)indolin-2-one derivatives and 2-(nitromethylene)imidazolidine under basic conditions (Cs₂CO₃) in ethanol. In addition, a diverse array of EDAM substrates (2b-2k) were tested in this reaction to afford the expected target compounds 5. This protocol is suitable for the combinatorial and parallel syntheses of natural-like products, including highly functionalized α-carbolines and pyrroles, especially 2-oxoindolin-3-yl pyrroles. This approach features several advantages, such as being a simple and practical operation (requiring only filtration and washing without column chromatography), furnishing excellent yields (72-98%), and producing diverse libraries of target compounds with potential biological activities.

Metal-Free [3+2] Annulation of Ynamides with Anthranils to Construct 2-Aminoindoles

A novel metal-free [3+2] annulation of ynamides with anthranils provides a facile, flexible, environmentally friendly, and atom-economical route to 2-aminoindoles. This synthetic process proceeds with efficiency, excellent regioselectivity, and wide functional group tolerance under mild conditions. Moreover, the obtained 2-aminoindole products represent a multifunctional platform for the construction of various 2-aminoindolyl frameworks.

Synthesis of quaternary carbon-centered indolo[1,2-a]quinazolinones and indazolo[1,2-a]indazolones via C-H functionalization

An unprecedented Ru(ii)-catalyzed Csp2-H bond activation and annulation reaction of phenylindazolones with diaryl-substituted alkynes and dialkyl-substituted alkynes provided efficient routes for the construction of all-carbon quaternary-centered indolo[1,2-a]quinazolinones and quaternary carbon-centered indazolo[1,2-a]indazolones, respectively. The indolo[1,2-a]quinazolinones were fomed via Csp2-H activation, alkyne insertion and a 1,2-phenyl shift. Indazolo[1,2-a]indazolones were formed through a cascade reaction via the formation of exocyclic double bonds containing indolo[1,2-a]quinazolinones.

Construction of isoxazolone-fused phenanthridines via Rh-catalyzed cascade C-H activation/cyclization of 3-arylisoxazolones with cyclic 2-diazo-1,3-diketones

A Rh(iii)-catalyzed cascade C-H activation/intramolecular cyclization of 3-aryl-5-isoxazolones with cyclic 2-diazo-1,3-diketones was described, leading to the formation of isoxazolo[2,3-f]phenanthridine skeletons. The protocol features the simultaneous one-pot formation of two new C-C/C-N bonds and one heterocycle in moderate-to-good yields with good functional group compatibility. It is amenable to large-scale synthesis and further transformation.

Expeditious Approach to Indoloquinazolinones via Double Annulations of o-Aminoacetophenones and Isocyanates

A novel procedure for a one-pot cascade reaction of o-aminoacetophenones and aryl/aliphatic isocyanates catalyzed/oxidized by the [Pd]/[Ag] system was developed. The reaction involves two C-N bond and one C-C bond formations during the double annulation process and the desired indoloquinazolinones and derivatives were afforded up to 81% yields from readily available substrates with a tolerance of a broad variety.

Nonmetal-catalyzed hydroamination of ynamides with amines

A TfOH-catalyzed hydroamination of ynamides with primary and secondary amines under mild reaction conditions is described for the efficient synthesis of N-arylimines and ethene-1,1-diamines.

Rh(iii)-Catalyzed sulfonylamination of α-indolyl alcohols via Csp2–Csp3 bond cleavage

A Rh(iii)-catalyzed beta-carbon amination of α-aryl alcohols with sulfonyl azides has been developed. This transformation features unstrained Csp²–Csp³ σ bond amination via C–C bond cleavage, and provides a direct approach to complex 2-aminoindoles.

Study on the interaction between 4-(1H-indol-3-yl)-2-(p-tolyl)quinazoline-3-oxide and human serum albumin

An organic small-molecular drug, 4-(1H-indol-3-yl)-2-(p-tolyl)quinazoline-3-oxide 1a was synthesized. It was employed to investigate the binding interaction and mechanism with human serum albumin (HSA). The experimental results indicated that the fluorescence quenching of HSA by 1a is a static quenching process and formation 1a-HSA complex. The site competition experiments revealed that the combination of 1a on HSA are hydrophobic interactions in the IIA domain and hydrogen bonds in IIIA domain of HSA, and the hydrophobic interactions of 1a on HSA are stronger than that of hydrogen bonds. These results were also confirmed by molecular docking theoretic analysis and ANS-hydrophobic fluorescent probe experiment. Synchronous fluorescence experiments showed that the polarity of HSA microenvironment was increase in the interaction process of 1a with HSA. The results of binding distance explored indicated that the combination distance between 1a and HSA is 3.63 nm, which is between 0.5R₀ and 1.5R₀, revealing the energy transfer between HSA and 1a is non-radiative. These results are very helpful for people to screen out high efficient indoloquinazoline drugs.

Organocatalyst in Direct C(sp2)-H Arylation of Unactivated Arenes: [1-(2-Hydroxyethyl)-piperazine]-Catalyzed Inter-/Intra-molecular C-H Bond Activation

This article describes the identification of 1-(2-hydroxyethyl)-piperazine as a new, cost-effective, highly efficient organocatalyst, which promotes both inter- and intra-molecular direct C(_sp²)-H arylations of unactivated arenes in the presence of potassium tert-butoxide. While the inter-molecular C-H arylation of unactivated benzenes with aryl halides (Ar-X; X = I, Br, Cl) toward biaryl syntheses underwent smoothly in the presence of only 10 mol % organocatalyst, the intra-molecular C-H arylation catalytic system composed of 40 mol % each of the catalyst and the additive (4-dimethylaminopyridine (DMAP)). The novel catalyst was also able to perform both inter- and intra-molecular direct arylations simultaneously in a single pot. The mechanistic studies confirmed the involvement of aryl radical anions and proceeded via a single-electron-transfer (SET) mechanism. The large substrate scope, high functional group tolerance, competition experiments, gram-scale synthesis, and kinetic studies further highlight the importance and versatile nature of the methodology as well as the compatibility of the new catalyst. To the best of our knowledge, this is the first report on any organocatalyst that reported detailed investigations of both inter- and intra-molecular direct C(_sp²)-H arylations of unactivated arenes in a single representation.

Structural insights for producing CK2α1-specific inhibitors

Casein kinase 2 catalytic subunit (CK2α) is classified into two subtypes CK2α1 and CK2α2. CK2α1 is a drug discovery target, whereas CK2α2 is an off-target of CK2α1 inhibitors. High amino acid sequence homology between these subtypes hampers efforts to produce ATP competitive inhibitors that are highly selective to CK2α1. Hematein was identified previously as a non-ATP-competitive inhibitor for CK2α1, whereas this compound acts as an ATP competitive CK2α2 inhibitor. Crystal structures of CK2α1 and CK2α2 in complex with hematein revealed distinct binding features that provide structural insights for producing CK2α1-selective inhibitors.

Novel Anthraquinone Derivatives as Dual Inhibitors of Topoisomerase 2 and Casein Kinase 2: In Silico Studies, Synthesis and Biological Evaluation on Leukemic Cell Lines

Background:

Cancer being a complex disease, single targeting agents remain unsuccessful. This calls for “multiple targeting”, wherein a single drug is so designed that it will modulate the activity of multiple protein targets. Topoisomerase 2 (Top2) helps in removing DNA tangles and super-coiling during cellular replication, Casein Kinase 2 (CK2) is involved in the phosphorylation of a multitude of protein targets. Thus, in the present work, we have tried to develop dual inhibitors of Top2 and CK2.

Objective:

With this view, in the present work, 2 human proteins, Top2 and CK2 have been targeted to achieve the anti-proliferative effects.

Methods:

Novel 1-acetylamidoanthraquinone (3a-3y) derivatives were designed, synthesized and their structures were elucidated by analytical and spectral characterization techniques (FTIR, 1H NMR, 13C NMR and Mass Spectroscopy). The synthesized compounds were then subjected to evaluation of cytotoxic potential by the Sulforhodamine B (SRB) protein assay, using HL60 and K562 cell lines. Ten compounds were analyzed for Top2, CK2 enzyme inhibitory potential. Further, top three compounds were subjected to cell cycle analysis.

Results:

The compounds 3a to 3c, 3e, 3f, 3i to 3p, 3t and 3x showed excellent cytotoxic activity to HL-60 cell line indicating their high anti-proliferative potential in AML. The compounds 3a to 3c, 3e, 3f, 3i to 3p and 3y have shown good to moderate activity on K-562 cell line. Compounds 3e, 3f, 3i, 3x and 3y were found more cytotoxic than standard doxorubicin. In cell cycle analysis, the cells (79-85%) were found to arrest in the G0/G1 phase.

Conclusion:

We have successfully designed, synthesized, purified and structurally characterized 1- acetylamidoanthraquinone derivatives. Even though our compounds need design optimization to further increase enzyme inhibition, their overall anti-proliferative effects were found to be encouraging.

Copper-catalyzed cross-dehydrogenative coupling between quinazoline-3-oxides and indoles

A novel and simple protocol for the synthesis of 4-(indole-3-yl)quinazolines via cross-dehydrogenative coupling of quinazoline-3-oxides and indoles under an air atmosphere has been developed.

A Network Pharmacology-Based Approach to Investigate the Novel TCM Formula against Huntington's Disease and Validated by Support Vector Machine Model

Several pathways are crucial in Huntington's disease (HD). Based on the concept of multitargets, network pharmacology-based analysis was employed to find out related proteins in disease network. The network target method aims to find out related mechanism of efficacy substances in rational design way. Traditional Chinese medicine prescriptions would be used for research and development against HD. Virtual screening was performed to obtain drug molecules with high binding capacity from traditional Chinese medicine (TCM) database@Taiwan. Quantitative structure-activity relationship (QSAR) models were conducted by MLR, SVM, CoMFA, and CoMSIA, constructed to predict the bioactivities of candidates. The compounds with high-dock score were further analyzed compared with control. Traditional Chinese medicine reported in the literature could be the training set provided for constructing novel formula by SVM model. We tried to find a novel formula that can bind well with these targets at the same time, which indicates our design could be highly related to the HD. Additionally, the candidates would validate by a long-term molecular dynamics (MD) simulation, 5 microseconds. Thus, we suggested the herbs Brucea javanica, Holarrhena antidysenterica, Dichroa febrifuga, Erythrophleum guineense, etc. which contained active compounds might be a novel medicine formula toward Huntington's disease.

Computational Approaches Towards Kinases as Attractive Targets for Anticancer Drug Discovery and Development

BACKGROUND

One of the major goals of computational chemists is to determine and develop the pathways for anticancer drug discovery and development. In recent past, high performance computing systems elicited the desired results with little or no side effects. The aim of the current review is to evaluate the role of computational chemistry in ascertaining kinases as attractive targets for anticancer drug discovery and development.

METHODS

Research related to computational studies in the field of anticancer drug development is reviewed. Extensive literature on achievements of theorists in this regard has been compiled and presented with special emphasis on kinases being the attractive anticancer drug targets.

RESULTS

Different approaches to facilitate anticancer drug discovery include determination of actual targets, multi-targeted drug discovery, ligand-protein inverse docking, virtual screening of drug like compounds, formation of di-nuclear analogs of drugs, drug specific nano-carrier design, kinetic and trapping studies in drug design, multi-target QSAR (Quantitative Structure Activity Relationship) model, targeted co-delivery of anticancer drug and siRNA, formation of stable inclusion complex, determination of mechanism of drug resistance, and designing drug like libraries for the prediction of drug-like compounds. Protein kinases have gained enough popularity as attractive targets for anticancer drugs. These kinases are responsible for uncontrolled and deregulated differentiation, proliferation, and cell signaling of the malignant cells which result in cancer.

CONCLUSION

Interest in developing drugs through computational methods is a growing trend, which saves equally the cost and time. Kinases are the most popular targets among the other for anticancer drugs which demand attention. 3D-QSAR modelling, molecular docking, and other computational approaches have not only identified the target-inhibitor binding interactions for better anticancer drug discovery but are also designing and predicting new inhibitors, which serve as lead for the synthetic preparation of drugs. In light of computational studies made so far in this field, the current review highlights the importance of kinases as attractive targets for anticancer drug discovery and development.

Integration of Lead Discovery Tactics and the Evolution of the Lead Discovery Toolbox

There has been much debate around the success rates of various screening strategies to identify starting points for drug discovery. Although high-throughput target-based and phenotypic screening has been the focus of this debate, techniques such as fragment screening, virtual screening, and DNA-encoded library screening are also increasingly reported as a source of new chemical equity. Here, we provide examples in which integration of more than one screening approach has improved the campaign outcome and discuss how strengths and weaknesses of various methods can be used to build a complementary toolbox of approaches, giving researchers the greatest probability of successfully identifying leads. Among others, we highlight case studies for receptor-interacting serine/threonine-protein kinase 1 and the bromo- and extra-terminal domain family of bromodomains. In each example, the unique insight or chemistries individual approaches provided are described, emphasizing the synergy of information obtained from the various tactics employed and the particular question each tactic was employed to answer. We conclude with a short prospective discussing how screening strategies are evolving, what this screening toolbox might look like in the future, how to maximize success through integration of multiple tactics, and scenarios that drive selection of one combination of tactics over another.

Discovery of 2,6-disubstituted pyrazine derivatives as inhibitors of CK2 and PIM kinases

The design and synthesis of a novel series of 2,6-disubstituted pyrazine derivatives as CK2 kinase inhibitors is described. Structure-guided optimization of a 5-substituted-3-thiophene carboxylic acid screening hit (3a) led to the development of a lead compound (12b), which shows inhibition in both enzymatic and cellular assays. Subsequent design and hybridization efforts also led to the unexpected identification of analogs with potent PIM kinase activity (14f).

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit water molecules that are the closest to the ligand in each frame of a molecular dynamics trajectory. This method demonstrated improved correlations between calculated and experimental binding energies in both protein-protein interactions and ligand-receptor complexes, in comparison to the standard MM-GBSA. A protocol optimization, aimed to maximize efficacy and efficiency, is discussed here considering penicillopepsin, HIV1-protease, and BCL-XL as test cases. Calculations were performed in triplicates on both classic HPC environments and on standard workstations equipped by a GPU card, evidencing no statistical differences in the results. No relevant differences in correlation to experiments were also observed when performing Nwat-MMGBSA calculations on 4 or 1 ns long trajectories. A fully automatic workflow for structure-based virtual screening, performing from library set-up to docking and Nwat-MMGBSA rescoring, has then been developed. The protocol has been tested against no rescoring or standard MM-GBSA rescoring within a retrospective virtual screening of inhibitors of AmpC β-lactamase and of the Rac1-Tiam1 protein-protein interaction. In both cases, Nwat-MMGBSA rescoring provided a statistically significant increase in the ROC AUCs of between 20 and 30%, compared to docking scoring or to standard MM-GBSA rescoring.

A novel allosteric site in casein kinase 2α discovered using combining bioinformatics and biochemistry methods

Casein kinase 2 (CK2) is a highly pleiotropic serine-threonine kinase, which catalyzed phosphorylation of more than 300 proteins that are implicated in regulation of many cellular functions, such as signal transduction, transcriptional control, apoptosis and the cell cycle. On the other hand, CK2 is abnormally elevated in a variety of tumors, and is considered as a promising therapeutic target. The currently available ATP-competitive CK2 inhibitors, however, lack selectivity, which has impeded their development in cancer therapy. Because allosteric inhibitors can avoid the shortcomings of conventional kinase inhibitors, this study was aimed to discover a new allosteric site in CK2α and to investigate the effects of mutations in this site on the activity of CK2α. Using Allosite based on protein dynamics and structural alignment, we predicted a new allosteric site that was partly located in the αC helix of CK2α. Five residues exposed on the surface of this site were mutated to validate the prediction. Kinetic analyses were performed using a luminescent ADP detection assay by varying the concentrations of a peptide substrate, and the results showed that the mutations I78C and I78W decreased CK2α activity, whereas V31R, K75E, I82C and P109C increased CK2α activity. Potential allosteric pathways were identified using the Monte Carlo path generation approach, and the results of these predicted allosteric pathways were consistent with the mutation analysis. Multiple sequence alignments of CK2α with the other kinases in the family were conducted using the ClustalX method, which revealed the diversity of the residues in the site. In conclusion, we identified a new allosteric site in CK2α that can be altered to modulate the activity of the kinase. Because of the high diversity of the residues in the site, the site can be targeted using rational drug design of specific CK2α inhibitors for biological relevance.

NIS Mediated Cross-Coupling of C(sp2)-H and N-H Bonds: A Transition-Metal-Free Approach toward Indolo[1,2-a]quinazolinones

A metal- and base-free protocol for intramolecular cross-coupling of C(sp²)-H and N-H bonds using N-iodosuccinimide (NIS) has been demonstrated. This environmentally benign approach furnishes a series of substituted indolo[1,2-a]quinazolinones from the suitably fabricated indoles via C-N bond forming cyclization in 28-82% yield. A plausible mechanism is proposed for this cyclization based on the results of a control experiment. This methodology requires no additional metal catalyst, oxidant, or base. Furthermore, the synthetic utility of the protocol is demonstrated by performing a gram scale reaction.

The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design

Casein kinase II (CK2) is an ubiquitous and pleiotropic serine/threonine protein kinase able to phosphorylate hundreds of substrates. Being implicated in several human diseases, from neurodegeneration to cancer, the biological roles of CK2 have been intensively studied. Upregulation of CK2 has been shown to be critical to tumor progression, making this kinase an attractive target for cancer therapy. Several CK2 inhibitors have been developed so far, the first being discovered by "trial and error testing". In the last decade, the development of in silico rational drug design has prompted the discovery, de novo design and optimization of several CK2 inhibitors, active in the low nanomolar range. The screening of big chemical libraries and the optimization of hit compounds by Structure Based Drug Design (SBDD) provide telling examples of a fruitful application of rational drug design to the development of CK2 inhibitors. Ligand Based Drug Design (LBDD) models have been also applied to CK2 drug discovery, however they were mainly focused on methodology improvements rather than being critical for de novo design and optimization. This manuscript provides detailed description of in silico methodologies whose applications to the design and development of CK2 inhibitors proved successful and promising.

Rational Drug Design Rational Drug Design

For the past three decades rationale drug design (RDD) has been developing as an innovative, rapid and successful way to discover new drug candidates. Many strategies have been followed and several targets with diverse structures and different biological roles have been investigated. Despite the variety of computational tools available, one can broadly divide them into two major classes that can be adopted either separately or in combination. The first class involves structure-based drug design, when the target's 3-dimensional structure is available or it can be computationally generated using homology modeling. On the other hand, when only a set of active molecules is available, and the structure of the target is unknown, ligand-based drug design tools are usually used. This review describes some recent advances in rational drug design, summarizes a number of their practical applications, and discusses both the advantages and shortcomings of the various techniques used.

An Ullmann N-arylation/2-amidation cascade by self-relay copper catalysis: one-pot synthesis of indolo[1,2-a]quinazolinones

We have developed a self-relay copper(i)-catalyzed Ullmann N-arylation/2-amidation cascade to form functionalized indolo[1,2-a]quinazolinones in one-pot from easily available indoles with 2-bromobenzamides.

Computational methods in drug discovery

The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.