Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human ß-Tubulin Isotypes.

Microtubules, composed of α- and ß-tubulin subunits are crucial for cell division with their dynamic tissue-specificity which is dictated by expression of isotypes. These isotypes differ in carboxy-terminal tails (CTTs), rich in negatively charged acidic residues in addition to the differences in the composition of active site residues. 2-Methoxy estradiol (2-ME) is the first antimicrotubule agent that showed less affinity toward hemopoietic-specific ß1 isotype consequently preventing myelosuppression toxicity. The present study focuses on the MD-directed conformational analysis of 2-ME and estimation of its binding affinity in the colchicine binding pocket of various ß-tubulin isotypes combined with the α-tubulin isotype, α1B. AlphaFold 2.0 was used to predict the 3D structure of phylogenetically divergent human ß-tubulin isotypes in dimer form with α1B. The dimeric complexes were subjected to induced-fit docking with 2-ME. The statistical analysis of docking showed differences in the binding characteristics of 2-ME with different isotypes. The replicas of atom-based molecular dynamic simulations of the best conformation of 2-ME provided insights into the molecular-level details of its binding pattern across the isotypes. Furthermore, the MM/GBSA analyses revealed the specific binding energy profile of 2-ME in ß-tubulin isotypes. It also highlighed, 2-ME exhibits the lowest binding affinity toward the ß1 isotype as supported by experimental study. The present study may offer useful information for designing next-generation antimicrotubule agents that are more specific and less toxic.

The Role of Water Network Chemistry in Proteins: A Structural Bioinformatics Perspective in Drug Discovery and Development.

BACKGROUND: Although water is regarded as a simple molecule, its ability to create hydrogen bonds makes it a highly complex molecule that is crucial to molecular biology. Water molecules are extremely small and are made up of two different types of atoms, each of which plays a particular role in biological processes. Despite substantial research, understanding the hydration chemistry of protein-ligand complexes remains difficult. Researchers are working on harnessing water molecules to solve unsolved challenges due to the development of computer technologies. OBJECTIVES: The goal of this review is to highlight the relevance of water molecules in protein environments, as well as to demonstrate how the lack of well-resolved crystal structures of proteins functions as a bottleneck in developing molecules that target critical therapeutic targets. In addition, the purpose of this article is to provide a common platform for researchers to consider numerous aspects connected to water molecules. CONCLUSION: Considering structure-based drug design, this review will make readers aware of the different aspects related to water molecules. It will provide an amalgamation of information related to the protein environment, linking the thermodynamic fingerprints of water with key therapeutic targets. It also demonstrates that a large number of computational tools are available to study the water network chemistry with the surrounding protein environment. It also emphasizes the need for computational methods in addressing gaps left by a poorly resolved crystallized protein structure.

Computational and Biological Investigations on Abl1 Tyrosine Kinase: A Review.

Abl1 tyrosine kinase is a validated target for the treatment of chronic myeloid leukemia. It is a form of cancer that is difficult to treat and much research is being done to identify new molecular entities and to tackle drug resistance issues. In recent years, drug resistance of Abl1 tyrosine kinase has become a major healthcare concern. Second and third-generation TKI reported better responses against the resistant forms; still they had no impact on long-term survival prolongation. New compounds derived from natural products and organic small molecule inhibitors can lay the foundation for better clinical therapies in the future. Computational methods, experimental and biological studies can help us understand the mechanism of drug resistance and identify novel molecule inhibitors. ADMET parameters analysis of reported drugs and novel small molecule inhibitors can also provide valuable insights. In this review, available therapies, point mutations, structure-activity relationship and ADMET parameters of reported series of Abl1 tyrosine kinase inhibitors and drugs are summarised. We summarise in detail recent computational and molecular biology studies that focus on designing drug molecules, investigation of natural product compounds and organic new chemical entities. Current ongoing research suggests that selective targeting of Abl1 tyrosine kinase at the molecular level to combat drug resistance in chronic myeloid leukemia is promising.

Inclusion complex of erlotinib with sulfobutyl ether-ß-cyclodextrin: Preparation, characterization, in silico, in vitro and in vivo evaluation.

The aim of the study was to investigate the impact of erlotinib sulfobutyl ether beta-cyclodextrin complex (ERL-SBE-ß-CD) on ERL dissolution rate and oral bioavailability. Preliminary comparative phase solubility study indicated ERL exhibited maximum solubility in SBE-ß-CD solution. Optimal experimental design confirmed freeze drying of SBE-ß-CD:ERL in 1:1.05 molar ratio as the optimum method. Differential scanning calorimetry (DSC), Fourier transformation infrared spectroscopy (FT-IR), powder X-ray diffractometry (PXRD), proton nuclear magnetic resonance ((1)H NMR) and two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY NMR) confirmed the inclusion complexation. The in silico computational study, employed to analyze the comparative interactions of ERL with SBE-ß-CD and ß-CD, indicated ease of ERL-SBE-ß-CD complexation. In vitro dissolution and in vivo bioavailability studies further confirmed the ERL-SBE-ß-CD as a valuable approach to enhance ERL oral bioavailability with 3.6-fold increase in relative oral bioavailability with higher Cmax (134.29 ± 36.51 vs. 42.36 ± 1.75 µg/ml) and AUC0-∞ (2103.47 ± 156.75 vs.580.43 ± 71.91 µg/ml h) over the free drug. The complex exhibited 3.2-fold increase in Cmax with 5.4-fold decrease in Tmax (0.5 ± 0.2 vs. 2.7 ± 0.8h) in comparison to pure ERL. Thus, ERL-SBE-ß-CD complexation exhibits a potential to enhance oral bioavailability of ERL leading to reduce dose and dose-related side effects.

Molecular dynamics approach to probe PKCßII-ligand interactions and influence of crystal water molecules on these interactions.

OBJECTIVE: PKCßII is a potential target for therapeutic intervention against pandemic diabetic complications. Present study probes the molecular interactions of PKCßII with its clinically important ligands, viz. ruboxistaurin, enzastaurin and co-crystallized ligand, 2-methyl-1H-indol-3-yl-BIM-1. RESEARCH DESIGN AND METHODS: The essentials of PKCßII-ligand interaction, crystal water-induced alterations in these interactions and key interacting flexible residues are analyzed. Computational methodologies, viz. molecular docking and molecular simulation coupled with molecular mechanics-Poisson-Boltzmann surface area and generalized born surface area (MM-PB[GB]SA) are employed. RESULTS: The structural changes in the presence and absence of crystal water molecules in PKCßII ATP binding site residues, and its interaction with bound ligand, are identified. Difference in interaction of selective and nonselective ligand with ATP binding site residues of PKCßII is reported. CONCLUSIONS: The study showed that the nonbonding interactions contribute significantly in PKCßII-ligand binding and presence of crystal water molecules affects the interactions. The findings of present work may integrate the new aspects in the drug design process of PKCßII inhibitors.

Protein kinase C inhibitors: a patent review (2010 - present).

INTRODUCTION: Protein kinase C (PKC) comprises at least 10 isoforms, pivotal in various cellular differentiation processes and in other specific cellular functions. Catalytic subunits of all PKCs are highly conserved which play a central role in the development of kinase-specific inhibitors for the treatment of a number of diseases and also in the drug resistance and immunological disorders. The authors' previous work of reviewing patents of PKC inhibitors is continued in this report. AREA COVERED: Thorough survey on the physiological roles of PKC isoforms and patents filed for PKC inhibitors from 2010 to present representing new and potential strategy for the cure and prevention of disorders due to elevation in various PKC levels is reported. EXPERT OPINION: The PKC isoforms are unique in terms of tissue distribution and an elevation in any isoform level results in different diseased conditions. Different PKC isoforms have high sequence identity but they are involved in different diseases. Crystal structure of few PKC isoforms viz. C1 domain of PKCδ, the C2 domains of PKCα and ß, kinase domain and full structure of PKCßII are known. Identification of more crystal structures and thorough analysis of available structures and information on the PKC ligands will be helpful in the drug designing and development processes.

Protein tyrosine phosphatase inhibitors: a patent review (2002 - 2011).

INTRODUCTION: The protein tyrosine phosphatases (PTPases or PTPs) are highly conserved phosphatases that regulate the tyrosine phosphorylation and consequently, the cellular functions. Protein tyrosine phosphorylation is the major post-translational modification to regulate signal transduction in cells. PTPs control diverse processes such as focal adhesion dynamics, cell-cell adhesion, insulin signaling, cytoskeletal functions, synaptogenesis and neurite growth. The availability of numerous X-ray crystal structures of PTPs, along with their inhibitors, has provided the opportunity for the structure-based design of effective inhibitors having potential for the treatment of various disorders. AREAS COVERED: The main focus of the present review is to get an insight into the most clinically relevant therapeutic PTP inhibitors published in patents over the past 10 years. EXPERT OPINION: Several computational studies are being carried out to understand ligand binding modes, selectivity interactions and conformational changes during inhibitor binding. PTP inhibitors that are of current interest include quinolyl, cyclic alabenzimidazole, pyrazine, (ethynediyl)bis-benzene, pyridopyrimidine, triazolopyridine, cyclo propylphenyl phenyloxamides, oxindole and azoloarin derivatives. The development of allosteric site-directed PTP inhibitors may help in understanding the absorption and selectivity of PTP inhibitors.

Rational design of CCR2 antagonists: a survey of computational studies.

IMPORTANCE OF THE FIELD: CC-chemokine receptor 2 (CCR2) belongs to the GPCR superfamily and is the primary receptor for monocyte chemoattractant protein-1 (MCP-1), also known as chemokine ligand CCL2. Studies indicate the possible involvement of MCP-1 and CCR2 in various disease conditions, such as rheumatic arthritis, multiple sclerosis, vascular diseases, obesity and diabetes, via the inflammatory pathway. MCP-1 and CCR2 knockout mice under a broad range of stimuli exhibit deficient monocyte recruitment suggesting its potential role in inflammation. Overall, there is evidence that an impairment of monocyte trafficking in inflammation models occurs when there is a loss of MCP-1 effector function. This makes its receptor, CCR2, an attractive target for pharmaceutical research. Several small molecular CCR2 antagonists have been developed, particularly in the industry. AREAS COVERED IN THIS REVIEW: In this article, we have summarized the in silico work carried out in the area of CCR2 and reviewed mainly the computer aided drug design (CADD) studies reported on quantitative structure-activity relationship, homology modeling, molecular docking and virtual screening. WHAT THE READER WILL GAIN: A survey of computational studies for the rational design and development of CCR2 antagonists. TAKE HOME MESSAGE: CADD tools can be used to rationalize the identification of the potential leads and these techniques can be effectively applied in the rapid searching of novel and potent CCR2 antagonists.