3D-QSAR and docking studies on pyrazolo[4,3-h]qinazoline-3-carboxamides as cyclin-dependent kinase 2 (CDK2) inhibitors

Progress in Synthesis and Bioactivity Evaluation of Pyrazoloquinazolines

Background:

This paper reviews the research progress of pyrazoloquinazolines which widely used in the field of medicine and pesticide in recent years. Five types of pyrazoloquinazolines are introduced: pyrazolo [4,3-h]quinazolines, pyrazolo[1,5-c]quinazolines, pyrazolo[4,3-f]quinazolines, pyrazolo[1,5-a] quinazolines , pyrazolo[1,5-b]quinazolines, and their new progress in the synthesis methods and treatment of diseases.

Methodology:

The derivatives of pyrazoloquinazolines exhibit a wide range of pharmacological properties such as antibacterial, anticancer, antioxidants, anti-inflammatory, anti-diabetic, antiviral activities. Consequently, their syntheses have attracted significant interest. Various methodologies have been developed for the synthesis and functionalization of these class of compounds.

Conclusion:

In the present article, the relevant and recent advances in the field will be briefly covered.

In Silico Exploration of Aryl Halides Analogues as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and ADMET Screening

Purpose: In this review, a set of aryl halides analogs were identified as potent checkpoint kinase 1 (Chk1) inhibitors through a series of computer-aided drug design processes, to develop models with good predictive ability, highlight the important interactions between the ligand and the Chk1 receptor protein and determine properties of the new proposed drugs as Chk1 inhibitors agents.

Methods: Three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, molecular docking and absorption, distribution, metabolism, excretion and toxicity (ADMET) approaches are used to determine structure activity relationship and confirm the stable conformation on the receptor pocket.

Results: The statistical analysis results of comparative -molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models that employed for a training set of 24 compounds gives reliable values of Q² (0.70 and 0.94, respectively) and R² (0.68 and 0.96, respectively).

Conclusion: Computer–aided drug design tools used to develop models that possess good predictive ability, and to determine the stability of the observed and predicted molecules in the receptor pocket, also in silico of pharmacokinetic (ADMET) results shows good properties and bioavailability for these new proposed Chk1 inhibitors agents.

Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease

The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.

Synthesis and SAR of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as potent and selective CDK4/6 inhibitors

CDK4/6 pathway is an attractive target for development of anti-cancer drugs. Herein, we reported the design and synthesis of a series of 4,5-dihydro-1H-pyrazolo [4,3-h]quinazoline derivatives as selective CDK4/6 inhibitors. Applied with the optimizing strategy to the initial scaffold, it is found that compound 13n is able to selectively inhibit CDK4 and CDK6 with IC₅₀ values 0.01 and 0.026 μM, respectively. The compound showed good anti-proliferative activity when tested in a panel of tumor cell lines with CDK4/6 related mechanism of action, the results clearly suggest that compound 13n works much better than Ly2385219 which is a selective CDK4/6 inhibitor. This compound was also found to have favorable pharmacokinetic parameters. Taken together, compound 13n could be selected for further preclinical evaluation.

Recent advances on CDK inhibitors: An insight by means of in silico methods

The cyclin dependent kinases (CDKs) are a small family of serine/threonine protein kinases that can act as a potential therapeutic target in several proliferative diseases, including cancer. This short review is a survey on the more recent research progresses in the field achieved by using in silico methods. All the "armamentarium" available to the medicinal chemists (docking protocols and molecular dynamics, fragment-based, de novo design, virtual screening, and QSAR) has been employed to the discovery of new, potent, and selective inhibitors of cyclin dependent kinases. The results cited herein can be useful to understand the nature of the inhibitor-target interactions, and furnish an insight on the structural/molecular requirements necessary to achieve the required selectivity against cyclin dependent kinases over other types of kinases.

Fusion of Structure and Ligand Based Methods for Identification of Novel CDK2 Inhibitors

Cyclin dependent kinases play a central role in cell cycle regulation which makes them a promising target with multifarious therapeutic potential. CDK2 regulates various events of the eukaryotic cell division cycle, and the pharmacological evidence indicates that overexpression of CDK2 causes abnormal cell-cycle regulation, which is directly associated with hyperproliferation of cancer cells. Therefore, CDK2 is regarded as a potential target molecule for anticancer medication. Thus, to decline CDK2 activity by potential lead compounds has proved to be an effective treatment for cancer. The availability of a large number of X-ray crystal structures and known inhibitors of CDK2 provides a gateway to perform efficient computational studies on this target. With the aim to identify new chemical entities from commercial libraries, with increased inhibitory potency for CDK2, ligand and structure based computational drug designing approaches were applied. A druglike library of 50,000 compounds from ChemDiv and ChemBridge databases was screened against CDK2, and 110 compounds were identified using the parallel application of these models. On in vitro evaluation of 40 compounds, seven compounds were found to have more than 50% inhibition at 10 μM. MD studies of the hits revealed the stability of these inhibitors and pivotal role of Glu81 and Leu83 for binding with CDK2. The overall study resulted in the identification of four new chemical entities possessing CDK2 inhibitory activity.

Molecular docking and biological evaluation of some thioxoquinazolin-4(3H)-one derivatives as anticancer, antioxidant and anticonvulsant agents

Background

The quinazoline are an important class of medicinal compounds that possess a number of biological activities like anticancer, anticonvulsant and antioxidant etc.

Results

We evaluated the previously synthesized quinazoline derivatives 1–3 for their anticancer activities against three cancer cell lines (HepG2, MCF-7, and HCT-116). Among the tested compounds, quinazolines 1 and 3 were found to be more potent than the standard drug Vinblastine against HepG2 and MCF-7 cell lines. All the tested compounds had less antioxidant activity and did not exhibit any anticonvulsant activity. Also, molecular docking studies were performed to get an insight into the binding modes of the compounds with human cyclin-dependent kinase 2, butyrylcholinesterase enzyme, human gamma-aminobutyric acid receptor. These compounds showed better docking properties with the CDK2 as compared to the other two enzymes.

Conclusions

The overall study showed that thioxoquinazolines are suitable antitumor agents and they should be explored for other biological activities. Modification in the available lot of quinazoline and synthesis of its novel derivatives is essential to explore the potential of this class of compounds. The increase in the threat and with the emergence of drug resistance, it is important to explore and develop more efficacious drugs.

Pyrazoloquinazolines: Synthetic strategies and bioactivities

Numerous N-heterocycles are indisputably evidenced to exhibit myriad biological activities. In the recent past, attempts made to condense the various heterocycles have resulted in derivatives possessing better bioactivities. Among many such condensed heterocycles, pyrazoloquinazolines have managed to hold the attention of many researchers, owing to the broad spectrum of activities they portray. This review is the first of its kind to congregate the various pyrazoloquinazolines reported until now and categorizes these structurally isomeric classes into eleven different groups based on the fusion pattern of the ring such as [1,5-c], [5,1-b], [4,3-h], etc. Furthermore, this review is a concerted effort to highlight design, synthetic strategies as well as biological activities of each class of this condensed heterocycle. Structure-activity relationship studies and in silico approaches wherever reported have also been discussed. In addition, manuscript also offers scope for design, synthesis and generation of libraries of unreported classes of pyrazoloquinazolines for the biological evaluation.

The discovery of potentially selective human neuronal nitric oxide synthase (nNOS) Inhibitors: a combination of pharmacophore modelling, CoMFA, virtual screening and molecular docking studies

Neuronal nitric oxide synthase (nNOS) plays an important role in neurotransmission and smooth muscle relaxation. Selective inhibition of nNOS over its other isozymes is highly desirable for the treatment of neurodegenerative diseases to avoid undesirable effects. In this study, we present a workflow for the identification and prioritization of compounds as potentially selective human nNOS inhibitors. Three-dimensional pharmacophore models were constructed based on a set of known nNOS inhibitors. The pharmacophore models were evaluated by Pareto surface and CoMFA (Comparative Molecular Field Analysis) analyses. The best pharmacophore model, which included 7 pharmacophore features, was used as a search query in the SPECS database (SPECS^®, Delft, The Netherlands). The hit compounds were further filtered by scoring and docking. Ten hits were identified as potential selective nNOS inhibitors.

An in silico exploration of the interaction mechanism of pyrazolo[1,5-a]pyrimidine type CDK2 inhibitors

CDK2, which interacts with cyclin A and cyclin E, is an important member of the CDK family. Having been proved to be associated with many diseases for its vital role in cell cycle, CDK2 is a promising target of anti-cancer drugs dealing with cell cycle disorders. In the present work, a total of 111 pyrazolo[1,5-a]pyrimidines (PHTPPs) as CDK2/cyclin A inhibitors were studied to conduct three-dimensional quantitative structure-activity (3D-QSAR) analyses. The optimal comparative molecular similarity indices analysis (CoMSIA) model shows that Q(2) = 0.516, Rncv(2) = 0.912, Rpre(2) = 0.914, Rm(2) = 0.843, SEP = 0.812, SEE = 0.347 with 10 components using steric, hydrophobic and H-bond donor field descriptors, indicating its effective internal and external predictive capacity. The contour maps further indicate that (1) bulky substituents in R1 are beneficial while H-bond donor groups at this position are detrimental; (2) hydrophobic contributions in the R2 area are favorable; (3) large and hydrophilic groups are well tolerated at the R3 position (a close H-bond donor moiety is favorable while a distal H-bond donor moiety in this area is disfavored); (4) bulky and hydrophobic features in the R4 region are beneficial for the biological activities and (5) the 7-N-aryl substitution is crucial to boost the inhibitory activities of the PHTPP inhibitors. Finally, docking and MD simulations demostrate that PHTPP derivatives are stabilized in a 'flying bat' conformation mainly through the H-bond interactions and hydrophobic contacts. Comparative studies indicate that PHTPP derivatives fit well within the ATP binding cleft in CDK2, with the core heterocyclic ring overlapping significantly with the adenine group of ATP despite a small deflection. In comparison to numerous other inhibitors binding to the ATP pocket, PHTPP analogues follow the binding fashion of purine inhibitors of this kinase. It is anticipated that the binding mechanism and structural features of PHTPP inhibitors studied in the present work will benefit the discovery of more potent CDK2 inhibitors, and the valid pyrazolo[1,5-a]pyrimidine-7-N-yl inhibitors will soon emerge from the large number of screening programmes to enter in clinical studies.

3-Hy-droxy-1-[(morpholin-4-yl)meth-yl]pyridazin-6(1H)-one

In the title compound, C₉H₁₃N₃O₃, the morpholine ring adopts a chair conformation and its mean plane makes a dihedral angle of 68.00 (11)° with the pyridazine ring. The carbonyl O atom deviates from the plane of the pyridazine ring by 0.0482 (12) Å. An intra­molecular C—H⋯O hydrogen bond occurs. In the crystal, mol­ecules are linked by O—H⋯O and C—H⋯O hydrogen bonds, forming chains along [1-10].

Morpholin-4-ium hydrogen l-tartrate monohydrate

In the title compound, C₄H₁₀NO⁺·C₄H₅O₆⁻·H₂O, the morpholine ring adopts a chair conformation. In the crystal, the tartrate anions are linked via O—H⋯O hydrogen bonds, forming chains propagating along [101]. These chains are linked via N—H⋯O and O—H⋯O hydrogen bonds, involving the morpholinium cation and the water molecule, forming a three-dimensional network.

5-Methoxy-2-{[4-(morpholin-4-yl)phenyl]iminomethyl}phenol

In the title compound, C₁₈H₂₀N₂O₃, the dihedral angle between the two aromatic rings is 33.66 (6)°. The morpholine ring adopts a chair conformation. The mol­ecular structure is stabilized by an intra­molecular O—H⋯N hydrogen bond. In the crystal, mol­ecules are linked via weak inter­molecular C—H⋯O and C—H⋯π inter­actions.

2,4-Diiodo-6-{[4-(morpholin-4-yl)phenyl]iminomethyl}phenol

In the title compound, C(17)H(16)I(2)N(2)O(2), the two aromatic rings are almost coplanar [dihedral angle 2.57 (15)°]. The morpholine ring adopts a chair conformation. The mol-ecular structure is stabilized by an O-H⋯N hydrogen bond and the crystal packing exhibits weak inter-molecular C-H⋯O and π-π [centroid-to-centroid distances 3.663 (3)-4.073 (3) Å] inter-actions.

6-Chloro-3-nitro-N-(propan-2-yl)pyridin-2-amine

There are two mol­ecules in the asymmetric unit mol­ecule of the title compound, C₈H₁₀ClN₃O₂. Intra­molecular N—H⋯O hydrogen bonds stabilize the mol­ecular structure. There are no classical inter­molecular hydrogen bonds in the crystal structure.

4-(4-Nitrobenzyl)morpholine

In the title compound, C₁₁H₁₄N₂O₃, an inter­molecular inter­action between a nitro group O atom and a neighboring benzene ring helps to stabilize the crystal structure [N⋯centroid = 3.933 (2) Å]. No classical hydrogen bonds are observed in the crystal packing.

Combined 3D-QSAR modeling and molecular docking studies on pyrrole-indolin-2-ones as Aurora A kinase inhibitors

Aurora kinases have emerged as attractive targets for the design of anticancer drugs. 3D-QSAR (comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)) and Surflex-docking studies were performed on a series of pyrrole-indoline-2-ones as Aurora A inhibitors. The CoMFA and CoMSIA models using 25 inhibitors in the training set gave r(2) (cv) values of 0.726 and 0.566, and r(2) values of 0.972 and 0.984, respectively. The adapted alignment method with the suitable parameters resulted in reliable models. The contour maps produced by the CoMFA and CoMSIA models were employed to rationalize the key structural requirements responsible for the activity. Surflex-docking studies revealed that the sulfo group, secondary amine group on indolin-2-one, and carbonyl of 6,7-dihydro-1H-indol-4(5H)-one groups were significant for binding to the receptor, and some essential features were also identified. Based on the 3D-QSAR and docking results, a set of new molecules with high predicted activities were designed.

Molecular modeling studies on 11H-dibenz[b,e]azepine and dibenz[b,f][1,4]oxazepine derivatives as potent agonists of the human TRPA1 receptor

A computational strategy based on comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was performed on a series of the 11H-dibenz[b,e]azepine and dibenz[b,f][1,4]oxazepine derivatives as potent agonists of the human TRPA1 receptor. The CoMFA and CoMSIA models resulting from a 21 molecule training set gave r²(cv) values of 0.631 and 0.542 and r² values of 0.986 and 0.981, respectively. The statistically significant models were validated by a test set of five compounds with predictive r²(pred). values of 0.967 and 0.981 for CoMFA and CoMSIA, respectively. A systemic external validation was also performed on the established models. The information obtained from 3D counter maps could facilitate the design of more potent human TRPA1 receptor agonists.