Current Pharmaceutical Design - Volume 19, Issue 12, 2013

Inhibition of DNA methyltransferases (DNMTs) is a promising approach for the therapeutic treatment of cancer and other diseases. In this work, we review the recent progress on the molecular modeling and virtual screening toward the identification of key structural features associated with the enzyme inhibitory action of active compounds and to identify DNMT inhibitors with novel molecular scaffolds. We discuss the molecular Read More

Today, emerging and increasing resistance to antibiotics has become a threat to public health worldwide. Antimicrobial peptides own unique action mechanisms making peptide antibiotics an attractive therapeutic option against resistant bacteria. However, their high haemolytic activity lacks the selectivity required for a human antibiotic. Therefore, additional efforts are needed to develop new antimicrobial peptides that possess Read More

Guanine-rich sequences found in telomeres and oncogene promoters have the ability to form G-quadruplex structures. In this paper we describe the use of a virtual screening assay to search a database of FDA-approved compounds for compounds with the potential to bind G-quadruplex DNA. More than 750 telomerase inhibitors were identified in a literature search as acting through G-quadruplex stabilization, and from evaluat Read More

The scoring functions for protein-ligand interactions plays central roles in computational drug design, virtual screening of chemical libraries for new lead identification, and prediction of possible binding targets of small chemical molecules. An ideal scoring function for protein-ligand interactions is expected to be able to recognize the native binding pose of a ligand on the protein surface among decoy poses, and to accurately predi Read More

The comparison of macromolecular structures, in terms of functionalities, is a crucial step when aiming to identify potential docking sites. Drug designers require the identification of such docking sites for the binding of two proteins, in order to form a stable complex. This paper presents a review of current approaches to macromolecular structure comparison and docking, following an algorithmic approach. We describe te Read More

Neutrophil elastase, a serine proteinase from the chymotrypsin family, has been the object of comprehensive experimental and theoretical studies to develop efficient human neutrophil elastase inhibitors. The serine protease has been linked to the pathology of a variety of inflammatory diseases, making it an attractive target for the development of anti-inflammatory compounds. In this work, we have built a common bin Read More

Myeloperoxidase (MPO) is the most abundant heme protein in neutrophils, and MPO catalyzes hypochlorous acid (HOCl) formation. MPO inhibitors (MPOis) can be used to treat several diseases in which MPO and HOCl levels are elevated. The molecular details of several MPOis have not been extensively studied to elucidate their molecular recognition properties. In addition, it is not known whether MPO has only one binding sit Read More

Our structural understanding of the superfamily of G-protein coupled receptors, a group of targets of utmost pharmacological importance, has improved dramatically in the last few years. This was directly translated in an increase of both the number and the relevance of computer-assisted drug design efforts devoted to these receptors. The field, which had been greatly influenced by ligand-based methods, has experienced Read More

Quantitative structure-activity relationship study was performed to understand the inhibitory activity of a set of 192 vascular endothelial growth factor receptor-2 (VEGFR-2) compounds. QSAR models were developed using multiple linear regression (MLR) and partial least squares (PLS) as linear methods. While principal component - artificial neural networks (PC-ANN) modeling method with application of eigenvalue ranking Read More

Computer-aided drug design (CADD) plays significant roles in all stages of today's drug discovery. Many CADD technologies and methods were employed in finding promising hits against different targets during the past several decades. In this review, the most common molecular modeling methods applied to computer-aided drug design are discussed. However, how to effectively integrate these computational methods and Read More

Pancreatic cancer is one of lethal and poor prognostic malignancies. Due to the absence of effective detecting methods, quite a number of efforts have been made to improve a survival advantage for treatment in patients with pancreatic cancer. Over the past decade, single-agent gemcitabine and gemcitabine-containing combinations were considered standard first-line therapies for advanced pancreatic cancer. Although these Read More

Protein kinases, which play an important role in the regulation of the majority of cellular processes, especially those involved in cellular signal transduction, by catalyzing the phosphorylation of specific proteins, are the attractive targets of drug design in pharmaceuticals industry. Interestingly, up to 10% of proteins in the human kinome termed pseudokinases are predicted to be enzymatically inactive, but are still Read More

As one of the most valuable methods for drug design, homology modeling shows that protein structures are more conserved than protein sequences, that is, the proteins with high sequence identity have high structural similarity, but protein pairs GA88/GB88 and GA95/GB95 prove the opposite. The pairs GA88 and GB88 shares the 88% sequence identity, but display different structures, and the pair GA95 and GB95 with Read More

An accurate estimation of binding free energy between protein and ligand, is one of the most important issues in the drug discovery process. However, it is an arduous and hard process to obtain accurate energy, especially the experimentally relevant free energies for protein-ligand in solution, including a proper treatment of the long-range electrostatics and solvation effects that are involved in optimization of atomic n Read More

DARPins (designed ankyrin repeat proteins), new kinds of binding proteins, have the potential to overcome the defects of monoclonal antibodies, and hence may become the alternatives to antibodies and generate a novel therapeutic approach. DARPins can be selected to bind any given target proteins with high affinity and specificity. In the process of binding to target proteins, the reason why DARPins have high affinity to Read More

CRM1 (also referred as exportin1 or Xpo1) is a key member of the importin β superfamily of nuclear transport receptors. Its potential as therapeutic target has attracted significant attention in recent years. CRM1 controls the transport of a number of growth regulatory proteins and tumor suppressor proteins including p53, p21, FOXO, PI3K/AKT, Wnt/ß-catenin, AP-1 and NF-kB etc. The overexpression of CRM1 has bee Read More

Assessing whether a protein structure is a good target or not before actually doing structure-based drug design on it is an important step to speed up the ligand discovery process. This is known as the “druggability” or “ligandability” assessment problem that has attracted increasing interest in recent years. The assessment typically includes the detection of ligand-binding sites on the protein surface and the prediction of their ab Read More