Targets, trials and tribulations in Alzheimer therapeutics.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by abnormal accumulation of extracellular amyloid beta senile plaques and intracellular neurofibrillary tangles in the parts of the brain responsible for cognition. The therapeutic burden for the management of AD relies solely on cholinesterase inhibitors that provide only symptomatic relief. The urgent need for disease-modifying drugs has resulted in intensive research in this domain, which has led to better understanding of the disease pathology and identification of a plethora of new pathological targets. Currently, there are over a hundred and seventy clinical trials exploring disease modification, cognitive enhancement, and reduction of neuro-psychiatric complications. However, the path to developing safe and efficacious AD therapeutics has not been without challenges. Several clinical trials have been terminated in advanced stages due to lack of therapeutic translation or increased incidence of adverse events. This review presents an in-depth look at the various therapeutic targets of AD and the lessons learnt during their clinical assessment. Comprehensive understanding of the implication of modulating various aspects of Alzheimer brain pathology is crucial for development of drugs with potential to halt disease progression in Alzheimer therapeutics.

Metallic and polymeric green nanoplatforms in oncology.

Chemotherapy, the cornerstone of cancer treatment, although invaluable, is plagued with unbearable and occasionally life-threatening side effects due to its inability to discriminate between tumorous and healthy cells. Anticancer nanomedicines have gained prominence due to their site-specific delivery of chemotherapeutic agents. In comparison to traditional chemical and physical procedures, which add to the chemical burden of an already ailing body, biosynthesis of nanomaterials by plants and microorganisms has evolved as safer 'green' nano-manufacturing technology. While nanomedicines from plant extracts have been exhaustively researched, the use of microbes as potential nano factories for the production of metal nanoparticles has recently piqued interest. Many bacteria develop defence mechanisms to detoxify hazardous metal ions, which results in formation of nano scaled metals that can be used for numerous therapeutic applications. The intrinsic variability of microbiological systems, however, poses its own set of challenges, necessitating more stringent standardization protocols in order to create nanomaterials with reproducible attributes. In this paper, we review the emerging trends in the green biosynthesis of nanomaterials and their potential applicability in cancer therapeutics. We probe the microbial biosynthetic mechanistic pathways and the efforts taken to control the physicochemical characteristics of nanoparticles. The applications of metallic nanoparticles obtained from microbes as well as polymeric systems obtained from bacteria, fungi and seaweed in oncology are described in detail. The development of these nanomaterials as next-generation green anticancer drugs may result in a revolution in cancer therapeutics.

Structural fingerprinting of pleiotropic flavonoids for multifaceted Alzheimer's disease.

Alzheimer's disease has emerged as one of the most challenging neurodegenerative diseases associated with dementia, loss of cognitive functioning and memory impairment. Despite enormous efforts to identify disease modifying technologies, the repertoire of currently approved drugs consists of a few symptomatic candidates that are not capable of halting disease progression. Moreover, these single mechanism drugs target only a small part of the pathological cascade and do not address most of the etiological basis of the disease. Development of therapies that are able to simultaneously tackle all the multiple interlinked causative factors such as amyloid protein aggregation, tau hyperphosphorylation, cholinergic deficit, oxidative stress, metal dyshomeostasis and neuro-inflammation has become the focus of intensive research in this domain. Flavonoids are natural phytochemicals that have demonstrated immense potential as medicinal agents due to their multiple beneficial therapeutic effects. The polypharmacological profile of flavonoids aligns well with the multifactorial pathological landscape of Alzheimer's disease, making them promising candidates to overcome the challenges of this neurodegenerative disorder. This review presents a detailed overview of the pleiotropic biology of flavonoids favourable for Alzheimer therapeutics and the structural basis for these effects. Structure activity trends for several flavonoid classes such as flavones, flavonols, flavanones, isoflavones, flavanols and anthocyanins are comprehensively analyzed in detail and presented.

Therapeutic Peptides: Unravelling Conformational Dynamics by Systematic Application of Biophysical Techniques.

Peptide therapeutics represents one of the fastest-growing sectors in the pharmaceutical drugs pipeline, with an increasing number of regulatory approvals every year. Their pharmacological diversity, biocompatibility, high degree of potency and selectivity make them an attractive choice in several therapeutic areas, such as diabetes, cancer, immune, metabolic, cardiovascular and infectious diseases. However, the development of peptides as drugs presents its own set of challenges, necessitating extensive property optimization aimed at improving their drug-like properties and stability in biological environments. The discovery and development of innovative peptide therapeutic platforms entail the employment of several biophysical techniques, which monitor the structural as well as the functional integrity of peptides. Small structural changes of the bioactive peptides in response to the presence of various excipients can have a major impact on their pharmaceutical prowess, necessitating the use of analytical techniques for efficient quality control during development. Here we present some widely used methods, such as circular dichroism, fluorescence spectroscopy and multi-dimensional homo and heteronuclear nuclear magnetic resonance spectroscopy that form an integral part of therapeutic peptides development. The application of combination biophysical platforms ensures the maintenance of the appropriate folded structure, which is a prerequisite for the safety and efficacy of peptide pharmaceuticals.

Smart nanocomposite assemblies for multimodal cancer theranostics.

Despite great strides in anticancer research, performance statistics of current treatment modalities remain dismal, highlighting the need for safe, efficacious strategies for tumour mitigation. Non-invasive fusion technology platforms combining photodynamic, photothermal and hyperthermia therapies have emerged as alternate strategies with potential to meet many of the unmet clinical demands in the domain of cancer. These therapies make use of metallic and magnetic nanoparticles with light absorbing properties, which are manipulated to generate either reactive cytotoxic oxygen species or heat for tumour ablation. Combination therapies integrating light, heat and magnetism-mediated nanoplatforms with the conventional approaches of chemotherapy, radiotherapy and surgery are emerging as precision medicine for targeted interventions against cancer. This article aims to compile recent developments of advanced nanocomposite assemblies that integrate multimodal therapeutics for cancer treatment. Amalgamation of various effective, non-invasive technological platforms such as photodynamic therapy (PDT), photothermal therapy (PTT), magnetic hyperthermia (MHT), and chemodynamic therapy (CDT) have tremendous potential in presenting safe and efficacious solutions to the formidable challenges in cancer therapeutics.

Potential of triazines in Alzheimer's disease: A versatile privileged scaffold.

Triazines are six-membered privileged scaffolds that have been explored in drug discovery programs owing to their stability in biological media and robust reactivity. Their unique chemical properties have led to the exploration of the triazine-containing molecules for multifaceted disorders like Alzheimer's disease (AD). The pathology of AD involves the interplay of multiple biochemical events such as amyloid beta-aggregation, formation of reactive oxygen species, cholinergic degradation, and metal ion dysregulation. The growing incidence of AD, coupled with the limited availability of efficacious medicines, necessitates the identification of newer therapeutic approaches. Privileged scaffolds like triazines with the potential for multiple biological effects offer excellent alternatives to the treatment of multifactorial AD. The present review describes numerous triazine-containing molecules capable of modulating single as well as multiple pathological factors involved in AD. The analysis of structural features of these molecules can provide useful insights for developing newer therapies.

The pleiotropic peroxisome proliferator activated receptors: Regulation and therapeutics.

The Peroxisome proliferator-activated receptors (PPARs) are key regulators of metabolic events in our body. Owing to their implication in maintenance of homeostasis, both PPAR agonists and antagonists assume therapeutic significance. Understanding the molecular mechanisms of each of the PPAR isotypes in the healthy body and during disease is crucial to exploiting their full therapeutic potential. This article is an attempt to present a rational analysis of the multifaceted therapeutic effects and underlying mechanisms of isotype-specific PPAR agonists, dual PPAR agonists, pan PPAR agonists as well as PPAR antagonists. A holistic understanding of the mechanistic dimensions of these key metabolic regulators will guide future efforts to identify novel molecules in the realm of metabolic, inflammatory and immunotherapeutic diseases.

Design strategies, SAR, and mechanistic insight of Aurora kinase inhibitors in cancer.

Aurora kinases (AURKs) are serine/threonine protein kinases that play a critical role during cell proliferation. Three isoforms of AURKs reported in mammals include AURKA, AURKB, AURKC, and all share a similar C-terminal catalytic domain with differences in their subcellular location, substrate specificity, and function. Recent research reports indicate an elevated expression of these kinases in several cancer types highlighting their role as oncogenes in tumorigenesis. Inhibition of AURKs is an attractive strategy to design potent inhibitors modulating this target. The last few years have witnessed immense research in the development of AURK inhibitors with few FDA approvals. The current clinical therapeutic regime in cancer is associated with severe side-effects and emerging resistance to existing drugs. This has been the key driver of research initiatives toward designing more potent drugs that can potentially circumvent the emerging resistance. This review is a comprehensive summary of recent research on AURK inhibitors and presents the development of scaffolds, their synthetic schemes, structure-activity relationships, biological activity, and enzyme inhibition potential. We hope to provide the reader with an array of scaffolds that can be selected for further research work and mechanistic studies in the development of new AURK inhibitors.

Docking structurally similar analogues: Dealing with the false-positive.

Analogue design forms one of the mainstays of new drug discovery. A fast-follow on approach is commonly used by modern day drug discoverers on the quest of the best in class. Monitoring close structural analogues of the pioneering drug by an algorithm such as docking is fraught with the risk of returning false positives. In this paper, we present the case of two near-pharmacophoric analogues of the JAK3 inhibitor Tasocitinib which give positive docking prediction despite being inactive. Post-processing the docked poses with MM/GBSA and parallel computation of electrostatic potential maps point towards a potential weakening of one of the crucial hydrogen bonds (hinge) within the ATP-binding pocket of JAK3. Perturbing the bound ligands by molecular dynamics (MD) simulations show the complexes to be unstable with the analogues losing their original hold on the protein within 1.2 ns. A short post MD simulation dramatically improves the prediction value of docking runs, especially when dealing with 'me-too' analogues.

Molecular dynamic simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity.

Inhibition of normal cellular apoptosis or programed cell death is the hallmark of all cancers. Apoptotic dysregulation can result in numerous pathological conditions, such as cancers, autoimmune disorders, and neurodegeneration. Members of the BCL-2 family of proteins regulate the process of apoptosis by its promotion or inhibition and overexpression of the pro-survival anti-apoptotic proteins (Bcl-2, Bcl-xL, and Mcl-1) has been associated with tumor maintenance, growth and progression Small molecules and peptides which bind the BH3 binding groove of these proteins have been explored in the recent times for their anticancer potential. The first anticancer agents targeting this family of proteins were aimed primarily toward inhibition of Bcl-2. An elevated level of Mcl-1, despite Bcl-2 inhibition, continues to be a cause for resistance in most cancers. However, in silico exploration of Mcl-1 specific drugs and their associated mechanisms have not been clearly elucidated. In order to understand the same, we have carried out docking and molecular dynamic simulations on ABT-263 (Navitoclax), an orally active inhibitor of Bcl-2, Bcl-xL, and Bcl-w proteins; Obatoclax, a pan-Bcl-2 inhibitor as well as Maritoclax, an Mcl-1 specific inhibitor. Docking studies revealed that binding to the hydrophobic grooves is a prerequisite for action on the BCL protein and the binding mechanism and chemical space utilization dictates stability as well as specificity of the inhibitor molecular dynamic simulations showed that on binding, the α-helices of these proteins exhibited less fluctuations than loop regions, also hydrophobic contacts and hydrogen bonding were observed to be the predominant interactions in the drug-receptor complexes. Communicated by Ramaswamy H. Sarma.

Design, synthesis and biological evaluation of novel inosine 5'-monophosphate dehydrogenase (IMPDH) inhibitors.

This study is based on our attempts to further explore the structure-activity relationship (SAR) of VX-148 (3) in an attempt to identify inosine 5'-mono-phosphate dehydrogenase (IMPDH) inhibitors superior to mycophenolic acid. A five-point pharmacophore developed using structurally diverse, known IMPDH inhibitors guided further design of novel analogs of 3. Several conventional as well as novel medicinal chemistry strategies were tried. The combined structure- and ligand-based approaches culminated in a few analogs with either retained or slightly higher potency. The compounds which retained the potency were also checked for their ability to inhibit human peripheral blood mononuclear cells proliferation. This study illuminates the stringent structural requirements and strict SAR for IMPDH II inhibition.

Virtual and experimental high-throughput screening (HTS) in search of novel inosine 5'-monophosphate dehydrogenase II (IMPDH II) inhibitors.

IMPDH (Inosine 5'-monophosphate dehydrogenase) catalyzes a rate-limiting step in the de novo biosynthesis of guanine nucleotides. IMPDH inhibition in sensitive cell types (e.g., lymphocytes) blocks proliferation (by blocking RNA and DNA synthesis as a result of decreased cellular levels of guanine nucleotides). This makes it an interesting target for cancer and autoimmune disorders. Currently available IMPDH inhibitors such as mycophenolic acid (MPA, uncompetitive inhibitor) and nucleoside analogs (e.g., ribavirin, competitive inhibitor after intracellular activation by phosphorylation) have unfavorable tolerability profiles which limit their use. Hence, the quest for novel IMPDH inhibitors continues. In the present study, a ligand-based virtual screening using IMPDH inhibitor pharmacophore models was performed on in-house compound collection. A total of 50,000 virtual hits were selected for primary screen using in vitro IMPDH II inhibition up to 10 µM. The list of 2,500 hits (with >70 % inhibition) was further subjected to hit confirmation for the determination of IC(50) values. The hits obtained were further clustered using maximum common substructure based formalism resulting in 90 classes and 7 singletons. A thorough inspection of these yielded 7 interesting classes in terms of mini-SAR with IC(50) values ranging from 0.163 µM to little over 25 µM. The average ligand efficiency was found to be 0.3 for the best class. The classes thus discovered represent structurally novel chemotypes which can be taken up for further development.

Synthesis and biological evaluation of novel (4 or 5-aryl)pyrazolyl-indoles as inhibitors of interleukin-2 inducible T-cell kinase (ITK).

Interleukin-2 inducible T-cell kinase (ITK) is one of five kinases that belong to the Tec kinase family that plays an important role in T-cell and mast cell signaling. Various reports point to a role of ITK in the treatment of allergic asthma. For example, it was shown that mice lacking ITK have reduced airway hyperresponsiveness, inflammation and tracheal responses in an allergic asthma model. In this article, we disclose novel ITK inhibitors based on (4 or 5-aryl)pyrazolyl-indole scaffold that were also found to be selective for ITK over other kinases like IRK, CDK2, GSK3ss and PKA.

A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants.

Quantitative Structure-Activity Relationships (QSAR) are being used since decades for prediction of biological activity, lead optimization, classification, identification and explanation of the mechanisms of drug action, and prediction of novel structural leads in drug discovery. Though the technique has lived up to its expectations in many aspects, much work still needs to be done in relation to problems related to the rational design of peptides. Peptides are the drugs of choice in many situations, however, designing them rationally is a complicated task and the complexity increases with the length of their sequence. In order to deal with the problem of peptide optimization, one of our recently developed QSAR formalisms CoRIA (Comparative Residue Interaction Analysis) is being expanded and modified as: reverse-CoRIA (rCoRIA) and mixed-CoRIA (mCoRIA) approaches. In these methodologies, the peptide is fragmented into individual units and the interaction energies (van der Waals, Coulombic and hydrophobic) of each amino acid in the peptide with the receptor as a whole (rCoRIA) and with individual active site residues in the receptor (mCoRIA) are calculated, which along with other thermodynamic descriptors, are used as independent variables that are correlated to the biological activity by chemometric methods. As a test case, the three CoRIA methodologies have been validated on a dataset of diverse nonamer peptides that bind to the Class I major histocompatibility complex molecule HLA-A*0201, and for which some structure activity relationships have already been reported. The different models developed, and validated both internally as well as externally, were found to be robust with statistically significant values of r(2) (correlation coefficient) and r(2)(pred) (predictive r(2)). These models were able to identify all the structure activity relationships known for this class of peptides, as well uncover some new relationships. This means that these methodologies will perform well for other peptide datasets too. The major advantage of these approaches is that they explicitly utilize the 3D structures of small molecules or peptides as well as their macromolecular targets, to extract position-specific information about important interactions between the ligand and receptor, which can assist the medicinal and computational chemists in designing new molecules, and biologists in studying the influence of mutations in the target receptor on ligand binding.

Equilibrium unfolding of DLC8 monomer by urea and guanidine hydrochloride: Distinctive global and residue level features.

We present circular dichroism (CD), steady state fluorescence and multidimensional NMR investigations on the equilibrium unfolding of monomeric dynein light chain protein (DLC8) by urea and guanidine hydrochloride (GdnHCl). Quantitative analysis of the CD and fluorescence denaturation curves reveals that urea unfolding is a two-state process, whereas guanidine unfolding is more complex. NMR investigations in the native state and in the near native states created by low denaturant concentrations enabled residue level characterization of the early structural and dynamic perturbations by the two denaturants. Firstly, (15)N transverse relaxation rates in the native state indicate that the regions around N10, Q27, the loop between beta2 and beta4 strands, and K87 at the C-terminal are potential unfolding initiation sites in the protein. Amide and (15)N chemical shift perturbations indicate different accessibilities of the residues along the chain and help identify locations of the early perturbations by the two denaturants. Guanidine and urea are seen to interact at several sites some of which are different in the two cases. Notable among the common interaction site is that around K87 which is in close proximity to W54 on the protein structure, but the interaction modes of the two denaturants are different. The secondary chemical shifts indicate that the structural perturbation by 1M urea is small, compared to that by guanidine which is more encompassing over the length of the chain. The probable (phi, psi) changes at the individual residues have been calculated using the TALOS algorithm. It appears that the helices in the protein are significantly perturbed by guanidine. Further, comparison of the spectral density functions of the native and the two near native states in the two denaturants implicate greater loosening of the structure by guanidine as compared to that by urea, even though the structures are still in the native state ensemble. These differences in the early perturbations of the native state structure and dynamics by the two denaturants might direct the protein along different pathways, as the unfolding progresses on further increasing the denaturant concentration.

Solution conformation of Substance P antagonists-[D-Arg1, D-Trp7,9, Leu11]-SP, [D-Arg1, D-Pro2, D-Trp7,9, Leu11]-SP and [D-Pro2, D-Trp7,9]-SP by CD, NMR and MD simulations.

Substance P (SP) is an important neuropeptide involved in pain transmission and induction of inflammation. Its antagonists are being extensively investigated for their non-narcotic analgesic and anti-inflammatory activity. With a view towards better understanding the structural requirements of these analogs for efficient interaction with the SP receptor, the conformation of three SP antagonists [D-Arg1, D-Trp7,9, Leu11]-SP, [D-Arg1, D-Pro2, D-Trp7,9, Leu11]-SP and [D-Pro2, D-Trp7,9]-SP has been studied by CD, NMR and molecular dynamics (MD) simulations. All three peptides exhibit a high dependence of structure on the solvent. The molecules tend to adopt beta-turns in solvents like DMSO and H2O and form helices in a hydrophobic environment. A direct relation between the helix forming potential of these antagonists with their receptor binding potency has been observed.

The amino-terminal domain of human signal transducers and activators of transcription 1: overexpression, purification and characterization.

The dual functional signal transducers and activators of transcription (STAT) proteins are latent cytoplasmic transcription factors that play crucial roles in host defense. Animals that lack these proteins are highly susceptible to microbial and viral infections and chemically induced primary tumours. We have over expressed the amino-terminal domain of human STAT1 (hSTAT1) in Escherichia coli and purified it by affinity chromatography and gel filtration chromatography. The entire process has been monitored by gel electrophoresis. The pure protein has been characterized by mass spectrometry and 2-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Our results indicate that the N-terminus of hSTAT1 exists as a dimer in solution.

New set of orthogonal protecting groups for the modular synthesis of heparan sulfate fragments.

Six strategically chosen monosaccharide building blocks, which are protected by a novel set of four orthogonal protecting groups (Lev, Fmoc, TBDPS, and All), can be employed for the efficient synthesis of the 20 disaccharide moieties found in heparan sulfate. The properly protected disaccharide building blocks can be converted into glycosyl donors and acceptors, which can be used for the modular synthesis of a wide range of well-defined oligosaccharides that differ in sulfation pattern. [structure: see text]