Structurally disordered C-terminal residues of GTP cyclohydrolase II are essential for its enzymatic activity.

GTP cyclohydrolase II (GCHII) is one of the rate limiting enzymes in riboflavin biosynthesis pathway and is shown to be a potential drug target for most of the pathogens. Previous biochemical and structural studies have identified the active site residues and elucidated the steps involved in the catalytic mechanism of GCHII. However, the last ∼20-25 C-terminal residues of GCHII remains unstructured in all the crystal structures determined to date and their role in the catalytic activity, if any, remains elusive. Therefore, to understand the role of these unstructured C-terminal residues, a series of C-terminal deletion mutants of GCHII from Helicobacter pylori (hGCHII) were generated and their catalytic activity was compared with its wild-type. Surprisingly, none of the C-terminal deletion mutants shows any enzymatic activity indicating that these are essential for GCHII function. To get additional insights for such loss of activity, homology models of full-length and deletion mutants of hGCHII in complex with GTP, Mg2+, and Zn2+ were generated and subjected to molecular dynamics simulation studies. The simulation studies show that a conserved histidine at 190th position from the unstructured C-terminal region of hGCHII interacts with α-phosphate of GTP. We propose that His-190 may play a role in the hydrolysis of pyrophosphate from GTP and in releasing the product, DARP. In summary, we demonstrate that the unstructured C-terminal residues of GCHII are important for its enzymatic activity and must be considered during rational drug designing. Communicated by Ramaswamy H. Sarma.

Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches.

Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.

Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS.

3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg2+. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg2+ is still elusive. Therefore, mechanistic role played by Mg2+ in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg2+ have shown entry of Mg2+ from bulk solvent into active site. Presence of Mg2+ in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg2+ into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a "lid" covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg2+ suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors.

Binding and discerning interactions of PTP1B allosteric inhibitors: novel insights from molecular dynamics simulations.

The α7 helix is either disordered or missing in the three co-crystal structures of allosteric inhibitors with protein tyrosine phosphatase 1B (PTP1B). It was modeled in each complex using the open form of PTP1B structure and studied using molecular dynamics (MD) simulations for 25 ns. B-factor analysis of the residues sheds light on its disordered nature in the co-crystal structures. Further, the ability of inhibitors to act as allosteric inhibitor was studied and established using novel hydrogen bond criteria. The MD simulations were utilized to determine the relative importance of electrostatic and hydrophobic component in to the binding of inhibitors. It was revealed that the hydrophobic interactions predominantly drive the molecular recognition of these inhibitors. Per residue energy decomposition analysis attributed dissimilar affinities of three inhibitors to the several hydrogen bonds and non-bonded interactions. Among the secondary structure elements that surround the allosteric site, helices α6, α7 and loop α6-α7 were notorious in providing variable affinities to the inhibitors. A novel hydrophobic pocket lined by the α7 helix residues Val287, Asn289 and Trp291 was identified in the allosteric site. This study provides useful insights for the rational design of high affinity PTP1B allosteric inhibitors.

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.

Insights into the permeability of drugs and drug-like molecules from MI-QSAR and HQSAR studies.

Membrane-interaction QSAR (MI-QSAR) and Holographic QSAR (HQSAR) analyses have been performed on a diverse set of drugs and drug-like molecules. MI-QSAR combines a set of membrane-solute interaction properties calculated during molecular dynamics simulation with the set of classical solute descriptors to predict the biological behavior of drugs and drug-like molecules. HQSAR is a technique which employs fragment fingerprints or molecular holograms as predictive variables of biological activity. A data set of 60 structurally diverse molecules with permeability coefficients were used to construct significant MI-QSAR and HQSAR models of Caco-2 cell permeation. A statistically meaningful MI-QSAR model was obtained with r (2) = 0.805 and q (2) = 0.696. Subsequently, HQSAR models were developed on the same data set. The best HQSAR model (r (2) = 0.915, q (2) = 0.539) was obtained with fragment distinctions atom, bond, donor and acceptor with atom count 4 to 7. The predictions for training and test set molecules are in good agreement with experimental results and show the potential of models for untested compounds. This displays the importance of MI-QSAR and HQSAR analysis in estimating ADME properties characterized by the transport of solutes through biological membranes.

Probing interaction requirements in PTP1B inhibitors: a comparative molecular dynamics study.

Molecular dynamics studies were performed on eight different crystal structure complexes of protein tyrosine phosphatase 1B (PTP1B) to study energy components and interactions important for the binding of substrates/inhibitors. Calculation of the binding free energy and the different components was accomplished using molecular mechanics--Poisson-Boltzmann surface area and--generalized Born surface area methods. Free energy was decomposed into individual amino acid contribution to know the relative importance. Hydrogen-bond existence maps for individual ligands were monitored comprehensively. It is evident from flexibility studies that the complexes exhibit rigidity in WPD loop, which is the first prerequisite for PTP1B inhibition. The study suggests that for designing active site inhibitors, there should be an optimum balance between total electrostatic and van der Waals interactions. It is also established that for allosteric inhibitors, van der Waals interactions are significant in addition to electrostatic interactions that are responsible for strong binding affinity.

Computer-assisted methods in chemical toxicity prediction.

In Silico predictive ADME/Tox screening of compounds is one of the hottest areas in drug discovery. To provide predictions of compound drug-like characteristics early in modern drug-discovery decision making, computational technologies have been widely accepted to develop rapid high throughput in silico ADMET analysis. It is widely perceived that the early screening of chemical entities can significantly reduce the expensive costs associated with late stage failures of drugs due to poor ADME/Tox properties. Drug toxic effects are broadly defined to include toxicity, mutagenicity, carcinogenicity, teratogenicity, neurotoxicity and immunotoxicity. Toxicity prediction techniques and structure-activity relationships relies on the accurate estimation and representation of physico-chemical and toxicological properties. This review highlights some of the freely and commercially available softwares for toxicity predictions. The information content can be utilized as a guide for the scientists involved in the drug discovery arena.