Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists

Although stapled α-helical peptides can address challenging targets, their advancement is impeded by poor understandings for making them cell permeable while avoiding off-target toxicities. By synthesizing >350 molecules, we present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects. Key insights include a clear correlation between lipophilicity and permeability, removal of positive charge to avoid off-target toxicities, judicious anionic residue placement to enhance solubility/behavior, optimization of C-terminal length/helicity to enhance potency, and optimization of staple type/number to avoid polypharmacology. Workflow application gives peptides with >292x improved cell proliferation potencies and no off-target cell proliferation effects ( > 3800x on-target index). Application of these 'design rules' to a distinct Mdm2(X) peptide series improves ( > 150x) cellular potencies and removes off-target toxicities. The outlined workflow should facilitate therapeutic impacts, especially for those targets such as Mdm2(X) that have hydrophobic interfaces and are targetable with a helical motif.

A high-throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell-based assays

Cyclic peptides are poised to target historically difficult to drug intracellular protein-protein interactions, however, their general cell impermeability poses a challenge for characterizing function. Recent advances in microfluidics have enabled permeabilization of the cytoplasmic membrane by physical cell deformation (i.e., mechanoporation), resulting in intracellular delivery of impermeable macromolecules in vector- and electrophoretic-free approaches. However, the number of payloads (e.g., peptides) and/or concentrations delivered via microfluidic mechanoporation is limited by having to pre-mix cells and payloads, a manually intensive process. In this work, we show that cells are momentarily permeable (t 1/2 = 1.1-2.8 min) after microfluidic vortex shedding (μVS) and that lower molecular weight macromolecules can be cytosolically delivered upon immediate exposure after cells are processed/permeabilized. To increase the ability to screen peptides, we built a system, dispensing-microfluidic vortex shedding (DμVS), that integrates a μVS chip with inline microplate-based dispensing. To do so, we synced an electronic pressure regulator, flow sensor, on/off dispense valve, and an x-y motion platform in a software-driven feedback loop. Using this system, we were able to deliver low microliter-scale volumes of transiently mechanoporated cells to hundreds of wells on microtiter plates in just several minutes (e.g., 96-well plate filled in <2.5 min). We validated the delivery of an impermeable peptide directed at MDM2, a negative regulator of the tumor suppressor p53, using a click chemistry- and NanoBRET-based cell permeability assay in 96-well format, with robust delivery across the full plate. Furthermore, we demonstrated that DμVS could be used to identify functional, low micromolar, cellular activity of otherwise cell-inactive MDM2-binding peptides using a p53 reporter cell assay in 96- and 384-well format. Overall, DμVS can be combined with downstream cell assays to investigate intracellular target engagement in a high-throughput manner, both for improving structure-activity relationship efforts and for early proof-of-biology of non-optimized peptide (or potentially other macromolecular) tools.

Targeted degradation of PCNA outperforms stoichiometric inhibition to result in programed cell death

Biodegraders are targeted protein degradation constructs composed of mini-proteins/peptides linked to E3 ligase receptors. We gained deeper insights into their utility by studying Con1-SPOP, a biodegrader against proliferating cell nuclear antigen (PCNA), an oncology target. Con1-SPOP proved pharmacologically superior to its stoichiometric (non-degrading) inhibitor equivalent (Con1-SPOPmut) as it had more potent anti-proliferative effects and uniquely induced DNA damage, cell apoptosis, and necrosis. Proteomics showed that PCNA degradation gave impaired mitotic division and mitochondria dysfunction, effects not seen with the stoichiometric inhibitor. We further showed that doxycycline-induced Con1-SPOP achieved complete tumor growth inhibition in vivo. Intracellular delivery of mRNA encoding Con1-SPOP via lipid nanoparticles (LNPs) depleted endogenous PCNA within hours of application with nanomolar potency. Our results demonstrate the utility of biodegraders as biological tools and highlight target degradation as a more efficacious approach versus stoichiometric inhibition. Once in vivo delivery is optimized, biodegraders may be leveraged as an exciting therapeutic modality.

PbS/graphene hybrid nanostructures coated glassy carbon electrode for the electrochemical sensing of copper ions in aqueous solution

In this research, we have studied the electrochemical sensing of Cu(II) ions in aqueous solution using PbS/Graphene composite nanostructure coated glassy carbon electrode (GCE). The SEM-EDAX analysis revealed that the lead sulphide nanocrystals are homogeneously embedded on the graphene nanosheets with an uniform particle size of 100 nm, and the elements presents 92.32% and Lead content of 5.45% and Sulfur content of 0.91%. Raman spectra exhibits G with respect to the E2g sp² hybridized C-C and D band with respect to the A1g mode in the disordered edge region of the GNS. The composite nanostructure coated GCE (PbS/Graphene/GCE) was prepared and its performance in the existence of metal ions such us Cd(II),Pb(II), Mg(II), Cu(II) and Ni(II) was studied using the current voltage curves in double distilled water within the scan rates of 25 to 300mVs-¹. The PbS/Graphene coated carbon electrode exhibited the higher anodic and cathodic peak current for copper solution than the other metal ions studied, which various linearly proportional to concentration. The electrochemical sensing characteristics PbS/GNS/GCE was found to be significant towards detecting Cu²⁺ ion within the concentration range of 1 × 10^-4 to 1 × 10^-8 M, with a lowest sensing detection limit of 1 × 10^-8 M.

STUB1 is an intracellular checkpoint for interferon gamma sensing

Immune checkpoint blockade (ICB) leads to durable and complete tumour regression in some patients but in others gives temporary, partial or no response. Accordingly, significant efforts are underway to identify tumour-intrinsic mechanisms underlying ICB resistance. Results from a published CRISPR screen in a mouse model suggested that targeting STUB1, an E3 ligase involved in protein homeostasis, may overcome ICB resistance but the molecular basis of this effect remains unclear. Herein, we report an under-appreciated role of STUB1 to dampen the interferon gamma (IFNγ) response. Genetic deletion of STUB1 increased IFNGR1 abundance on the cell surface and thus enhanced the downstream IFNγ response as showed by multiple approaches including Western blotting, flow cytometry, qPCR, phospho-STAT1 assay, immunopeptidomics, proteomics, and gene expression profiling. Human prostate and breast cancer cells with STUB1 deletion were also susceptible to cytokine-induced growth inhibition. Furthermore, blockade of STUB1 protein function recapitulated the STUB1-null phenotypes. Despite these encouraging in vitro data and positive implications from clinical datasets, we did not observe in vivo benefits of inactivating Stub1 in mouse syngeneic tumour models-with or without combination with anti-PD-1 therapy. However, our findings elucidate STUB1 as a barrier to IFNγ sensing, prompting further investigations to assess if broader inactivation of human STUB1 in both tumors and immune cells could overcome ICB resistance.

Synthesis and characterization of 4-Halobenzylidene malanonitriles for optical detection of Nickel (II) ions in aqueous solution

In this work, we have developed fluorescent detection techniques for the determination of Ni²⁺ ions in aqueous medium with sensitivity using metal coordinating fluorescent molecules namely 4-Halobenzylidene malanonitrile. The halogen substituted benzylidene malanonitile were synthesised Knoevenagel condensation reaction of various halogen substituted aromatic aldehydes with malanonitrile and products were characterised by IR and NMR spectroscopy. The obtained benzylidene malanonitiles and are exhibited a fluorescent emission with a peak of 430 nm, 440 nm and 448 nm for chloro, bromo and fluoro substituted compounds, respectively. The intensity of optical emission of the studied molecules is increased proportional to the addition of Ni²⁺ ions. The effect of different halogen substitution on the fluorescence behaviour of benylidene malononitrile has also been investigated. The synthesised title compounds showed a lowest detection limit of 10^-20 M for the Nickel (II) ions in aqueous solution under UV-Vis absorption spectra. The molecule 4- Bromobenzylidene malanonitrile exhibited a lowest detection limit of 10^-19 M for the Nickel (II) ions in, aqueous solution, photoluminescence analysis.

Imaging features of Robert's uterus: Case series of a rare Mullerian duct anomaly

The diagnosis of Mullerian duct anomaly is crucial because of strong association with infertility, endometriosis and miscarriage. Robert's uterus is a rare variant of septate uterus. Patients present with recurrent abdominal pain and severe dysmenorrhoea. Magnetic resonance imaging is the investigation of choice. In this case series, we present the imaging features of four such cases.

NanoClick: A High Throughput, Target-Agnostic Peptide Cell Permeability Assay

Macrocyclic peptides open new opportunities to target intracellular protein-protein interactions (PPIs) that are often considered nondruggable by traditional small molecules. However, engineering sufficient membrane permeability into these molecules is a central challenge for identifying clinical candidates. Currently, there is a lack of high-throughput assays to assess peptide permeability, which limits our capacity to engineer this property into macrocyclic peptides for advancement through drug discovery pipelines. Accordingly, we developed a high throughput and target-agnostic cell permeability assay that measures the relative cumulative cytosolic exposure of a peptide in a concentration-dependent manner. The assay was named NanoClick as it combines in-cell Click chemistry with an intracellular NanoBRET signal. We validated the approach using known cell penetrating peptides and further demonstrated a correlation to cellular activity using a p53/MDM2 model system. With minimal change to the peptide sequence, NanoClick enables the ability to measure uptake of molecules that enter the cell via different mechanisms such as endocytosis, membrane translocation, or passive permeability. Overall, the NanoClick assay can serve as a screening tool to uncover predictive design rules to guide structure-activity-permeability relationships in the optimization of functionally active molecules.

De-risking Drug Discovery of Intracellular Targeting Peptides: Screening Strategies to Eliminate False-Positive Hits

Nonspecific promiscuous compounds can mislead researchers and waste significant resources. This phenomenon, though well-documented for small molecules, has not been widely explored for the peptide modality. Here we demonstrate that two purported peptide-based KRas inhibitors, SAH-SOS1 _A and cyclorasin 9A5, exemplify false-positive molecules-in terms of both their binding affinities and cellular activities. Through multiple gold-standard biophysical techniques, we unambiguously show that both peptides lack specific binding to KRas and instead induce protein unfolding. Although these peptides inhibited cellular proliferation, the activities appeared to be off-target on the basis of a counterscreen with KRas-independent cell lines. We further demonstrate that their cellular activities are derived from membrane disruption. Accordingly, we propose that to de-risk false-positive molecules, orthogonal binding assays and cellular counterscreens are indispensable.

Macrocyclization of an all-d linear α-helical peptide imparts cellular permeability

Peptide-based molecules hold great potential as targeted inhibitors of intracellular protein-protein interactions (PPIs). Indeed, the vast diversity of chemical space conferred through their primary, secondary and tertiary structures allows these molecules to be applied to targets that are typically deemed intractable via small molecules. However, the development of peptide therapeutics has been hindered by their limited conformational stability, proteolytic sensitivity and cell permeability. Several contemporary peptide design strategies are aimed at addressing these issues. Strategic macrocyclization through optimally placed chemical braces such as olefinic hydrocarbon crosslinks, commonly referred to as staples, may improve peptide properties by (i) restricting conformational freedom to improve target affinities, (ii) improving proteolytic resistance, and (iii) enhancing cell permeability. As a second strategy, molecules constructed entirely from d-amino acids are hyper-resistant to proteolytic cleavage, but generally lack conformational stability and membrane permeability. Since neither approach is a complete solution, we have combined these strategies to identify the first examples of all-d α-helical stapled and stitched peptides. As a template, we used a recently reported all d-linear peptide that is a potent inhibitor of the p53-Mdm2 interaction, but is devoid of cellular activity. To design both stapled and stitched all-d-peptide analogues, we used computational modelling to predict optimal staple placement. The resultant novel macrocyclic all d-peptide was determined to exhibit increased α-helicity, improved target binding, complete proteolytic stability and, most notably, cellular activity.

Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ s^Lab⟩ ≤ (0.15 ± 0.01) Da (1σ_x̅). All laboratories achieved ⟨s^Lab⟩ ≤ 0.4 Da. For immersions of protein at T_HDX = (3.6 to 25) °C and for D₂O exchange times of t_HDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σ_{reproducibility}^{15 Laboratories}( t_HDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at T_HDX = 25 °C exhibited reproducibility of σ_{reproducibility}^25C cohort( t_HDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.

Outcomes of patients with metastatic clear-cell renal cell carcinoma treated with second-line VEGFR-TKI after first-line immune checkpoint inhibitors

BACKGROUND

Immune checkpoint inhibitors (ICIs) are being increasingly utilised in the front-line (1L) setting of metastatic clear-cell renal cell carcinoma (mccRCC). Limited data exist on responses and survival on second-line (2L) vascular endothelial growth factor-receptor tyrosine kinase inhibitor (VEGFR-TKI) therapy after 1L ICI therapy.

PATIENTS AND METHODS

This is a retrospective study of mccRCC patients treated with 2L VEGFR-TKI after progressive disease (PD) with 1L ICI. Patients were treated at MD Anderson Cancer Center or Memorial Sloan Kettering Cancer Center between December 2015 and February 2018. Objective response was assessed by blinded radiologists' review using Response Evaluation Criteria in Solid Tumours v1.1. Descriptive statistics and Kaplan-Meier method were used.

RESULTS

Seventy patients were included in the analysis. Median age at mccRCC diagnosis was 59 years; 8 patients (11%) had international metastatic database consortium favourable-risk disease, 48 (69%) had intermediate-risk disease and 14 (20%) had poor-risk disease. As 1L therapy, 12 patients (17%) received anti-programmed death ligand-1 (PD-(L)1) monotherapy with nivolumab or atezolizumab, 33 (47%) received nivolumab plus ipilimumab and 25 (36%) received combination anti-PD-(L)1 plus bevacizumab. 2L TKI therapies included pazopanib, sunitinib, axitinib and cabozantinib. On 2L TKI therapy, one patient (1.5%) achieved a complete response, 27 patients (39.7%) a partial response and 36 patients (52.9%) stable disease. Median progression-free survival (mPFS) was 13.2 months (95% confidence interval: 10.1, NA). Forty-five percent of subjects required a dose reduction, and twenty-seven percent of patients discontinued treatment because of toxicity.

CONCLUSIONS

In this retrospective study of patients with mccRCC receiving 2L TKI monotherapy after 1L ICI, we observed 2L antitumour activity and tolerance comparable to historical data for 1L TKI.

Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb

The spreadsheet file reported herein provides centroid data, descriptive of deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS) method. The protein sample was incubated in deuterium-rich solutions under uniform pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic peptide fragments were measured by mass spectrometry. These data were reported by fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage. In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide sequences of the Fc fragment. The instrumentation and physical and chemical conditions under which these data were acquired are documented.

Can ARFI elastography be used to differentiate parathyroid from thyroid lesions?

OBJECTIVES

To assess if elasticity score (ES) and shear wave velocity (SWV) measurement obtained using ARFI elastography can differentiate between parathyroid lesions and thyroid nodules.

MATERIALS AND METHODS

ARFI elastography was performed on patients with primary hyperparathyroidism or solid thyroid nodules who were being considered for surgery using virtual touch quantification and virtual touch imaging (VTI) software. Only patients with surgical histopathology (47 parathyroid lesions, 38 benign thyroid nodules and 55 malignant thyroid nodules) were included for final analysis. SWV and ES of the parathyroid and thyroid nodules were compared and their ability to differentiate between parathyroid and thyroid was analyzed using receiver operating characteristic curve analysis.

RESULTS

There were 39 solitary adenomas, 2 double adenomas and 4 parathyroid hyperplasias with mean size of 19.6 ± 9.7 mm in 44 patients (21 male, 23 females) with primary hyperparathyroidism. The mean SWV of the parathyroid lesion (1.6 ± 0.78 m/s) was significantly different from benign (2.11 ± 0.8 m/s) and malignant (4.3 ± 2.71 m/s) thyroid nodules, p < 0.05; so was the ES, Chi square = 51.6, p < 0.001. The majority of parathyroid lesions (n = 37, 78.7%) had ES of 2 with speckled (n = 42, 89.3%) appearance, and none showed ES of 4. The diagnostic performance of speckled appearance on VTI, elasticity score and SWV measurements was 0.901, 0.724 and 0.797, respectively, to differentiate between parathyroid and thyroid lesions.

CONCLUSIONS

Parathyroid lesions are softer than thyroid nodules. A shear wave velocity of 1.72 m/s can differentiate between parathyroid lesions and thyroid nodules.

Hydrogen bonded charge transfer molecular salt (4-chloro anilinium-3-nitrophthalate) for photophysical and pharmacological applications

Radical scavenging activity against DPPH radical and binding properties of a hydrogen bonded charge transfer molecular salt 4-chloro anilinium-3-nitrophthalate(CANP) with calf thymus DNA has been studied by electronic absorption and emission spectroscopy. The molecular structure and crystallinity of the CANP salt have been established by carried out powder and single crystal X-ray diffraction analysis which indicated that cation and anion are linked through strong N⁺H^…O^- type of hydrogen bond. FTIR spectroscopic study was carried out to know the various functional groups present in the crystal. ¹H and ¹³C NMR spectra were recorded to further confirm the molecular structure of the salt crystal. The thermal stability of the title salt was established by TG/DTA analyses simultaneously on the powdered sample of the title crystal. Further, the CANP salt was examined against various bacteria and fungi strains which showed a remarkable antimicrobial activity compared to that of the standards Ciproflaxin and Clotrimazole. The results showed that the CANP salt could interact with CT-DNA through intercalation. Antioxidant studies of the substrates alone and synthesized CANP salt showed that the latter has been better radical scavenging activity than that of the former against DPPH radical. The third order nonlinear susceptibility of the CANP salt was established by the Z-scan study.

Epitope and Paratope Mapping Reveals Temperature-Dependent Alterations in the Dengue-Antibody Interface

Uncovering mechanisms of antibody-mediated neutralization for viral infections requires epitope and paratope mapping in the context of whole viral particle interactions with the antibody in solution. In this study, we use amide hydrogen/deuterium exchange mass spectrometry to describe the interface of a dengue virus-neutralizing antibody, 2D22, with its target epitope. 2D22 binds specifically to DENV2, a serotype showing strain-specific structural expansion at human host physiological temperatures of 37°C. Our results identify the heavy chain of 2D22 to be the primary determinant for binding DENV2. Temperature-mediated expansion alters the mode of interaction of 2D22 binding. Importantly, 2D22 interferes with the viral expansion process and offers a basis for its neutralization mechanism. The relative magnitude of deuterium exchange protection upon antibody binding across the various epitope loci allows a deconstruction of the antibody-viral interface in host-specific environments and offers a robust approach for targeted antibody engineering.

"PAUSE": a method for communicating radiological extent of peritoneal malignancy

Radiology reports of diffuse peritoneal disease should address key findings pertinent to the management of these patients. The reporting of radiology findings in patients with peritoneal malignancy is currently variable and poorly standardised. Using the acronym "PAUSE" we emphasise the key imaging features that a radiology report should include in a patient with peritoneal malignancy, focussing on the key elements determining feasibility and likely prognosis of surgery and potential benefits from cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). The term "PAUSE" incorporates the following: P, primary tumour and peritoneal carcinomatosis index (PCI) as estimated by imaging; A, ascites and abdominal wall involvement; U, unfavourable sites of involvement; S, small bowel and mesenteric disease; E, extra peritoneal metastases. Thus, "PAUSE" has the potential to standardise radiology reporting in this field.

Dissecting Orthosteric Contacts for a Reverse-Fragment-Based Ligand Design

Orthosteric sites on proteins are formed typically from noncontiguous interacting sites in three-dimensional space where the composite binding interaction of a biological ligand is mediated by multiple synergistic interactions of its constituent functional groups. Through these multiple interactions, ligands stabilize both the ligand binding site and the local secondary structure. However, relative energetic contributions of the individual contacts in these protein-ligand interactions are difficult to resolve. Deconvolution of the contributions of these various functional groups in natural inhibitors/ligand would greatly aid in iterative fragment-based drug discovery (FBDD). In this study, we describe an approach of progressive unfolding of a target protein using a gradient of denaturant urea to reveal the individual energetic contributions of various ligand-functional groups to the affinity of the entire ligand. Through calibrated unfolding of two protein-ligand systems: cAMP-bound regulatory subunit of Protein Kinase A (RIα) and IBMX-bound phosphodiesterase8 (PDE8), monitored by amide hydrogen-deuterium exchange mass spectrometry, we show progressive disruption of individual orthosteric contacts in the ligand binding sites, allowing us to rank the energetic contributions of these individual interactions. In the two cAMP-binding sites of RIα, exocyclic phosphate oxygens of cAMP were identified to mediate stronger interactions than ribose 2'-OH in both the RIα-cAMP binding interfaces. Further, we have also ranked the relative contributions of the different functional groups of IBMX based on their interactions with the orthosteric residues of PDE8. This strategy for deconstruction of individual binding sites and identification of the strongest functional group interaction in enzyme orthosteric sites offers a rational starting point for FBDD.

Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design

A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites. This assumes a greater challenge when considering the interactions of low affinity ligands (dissociation constants, K_D, in the μM range or lower). Amide hydrogen deuterium Exchange mass spectrometry (HDXMS) is a robust method that can provide both structural insights and dynamics information on both high affinity and transient protein-ligand interactions. In this study, an application of HDXMS for probing the dynamics of low affinity ligands to proteins is described using the N-terminal ATPase domain of Hsp90. Comparison of Hsp90 dynamics between high affinity natural inhibitors (K_D ~ nM) and fragment compounds reveal that HDXMS is highly sensitive in mapping the interactions of both high and low affinity ligands. HDXMS reports on changes that reflect both orthosteric effects and allosteric changes accompanying binding. Orthosteric sites can be identified by overlaying HDXMS onto structural information of protein-ligand complexes. Regions distal to orthosteric sites indicate long range conformational changes with implications for allostery. HDXMS, thus finds powerful utility as a high throughput method for compound library screening to identify binding sites and describe allostery with important implications for fragment-based ligand discovery (FBLD).

Ligand interactions with proteins result in broad changes that are propagated throughout the target proteins, across space and time. These changes can be broadly classified into: orthosteric effects at the ligand binding site and allosteric changes at distal sites. These allosteric changes are difficult to localize and distinguish from binding interactions. In this study, we describe the application of amide hydrogen/deuterium exchange mass-spectrometry (HDXMS) to differentiate between changes occurring at the binding site and at distal allosteric sites by combining HDXMS with X-ray crystallography. Every ligand or a fragment mediates distinct contacts and results in changes in deuterium uptake across the protein. By comparing with orthosteric structural information, it is possible to identify long-range changes (action at a distance) due to the ligands. An important application of HDXMS is that it can identify subtle changes in protein dynamics that cannot be picked up by quantitative screens of protein-ligand interactions or crystal structures. This gives us the ability to describe ligand binding based on the response from different regions in the proteins. Thus it provides us with the potential to accurately measure and compare changes in dynamics upon binding different ligands and fragments, which is greatly valuable in fragment-based ligand design.

Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution

Infection by the four serotypes of Dengue virus (DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all four Dengue virus serotypes in solution are presented for the first time. The solution models derived revealed an arrangement of the full-length NS5 (NS5FL) proteins with the MTase domain positioned at the top of the RdRP domain. The DENV-1 to DENV-4 NS5 forms are elongated and flexible in solution, with DENV-4 NS5 being more compact relative to NS5 from DENV-1, DENV-2 and DENV-3. Solution studies of the individual MTase and RdRp domains show the compactness of the RdRp domain as well as the contribution of the MTase domain and the ten-residue linker region to the flexibility of the entire NS5. Swapping the ten-residue linker between DENV-4 NS5FL and DENV-3 NS5FL demonstrated its importance in MTase-RdRp communication and in concerted interaction with viral and host proteins, as probed by amide hydrogen/deuterium mass spectrometry. Conformational alterations owing to RNA binding are presented.

Parallel Allostery by cAMP and PDE Coordinates Activation and Termination Phases in cAMP Signaling

The second messenger molecule cAMP regulates the activation phase of the cAMP signaling pathway through high-affinity interactions with the cytosolic cAMP receptor, the protein kinase A regulatory subunit (PKAR). Phosphodiesterases (PDEs) are enzymes responsible for catalyzing hydrolysis of cAMP to 5' AMP. It was recently shown that PDEs interact with PKAR to initiate the termination phase of the cAMP signaling pathway. While the steps in the activation phase are well understood, steps in the termination pathway are unknown. Specifically, the binding and allosteric networks that regulate the dynamic interplay between PKAR, PDE, and cAMP are unclear. In this study, PKAR and PDE from Dictyostelium discoideum (RD and RegA, respectively) were used as a model system to monitor complex formation in the presence and absence of cAMP. Amide hydrogen/deuterium exchange mass spectrometry was used to monitor slow conformational transitions in RD, using disordered regions as conformational probes. Our results reveal that RD regulates its interactions with cAMP and RegA at distinct loci by undergoing slow conformational transitions between two metastable states. In the presence of cAMP, RD and RegA form a stable ternary complex, while in the absence of cAMP they maintain transient interactions. RegA and cAMP each bind at orthogonal sites on RD with resultant contrasting effects on its dynamics through parallel allosteric relays at multiple important loci. RD thus serves as an integrative node in cAMP termination by coordinating multiple allosteric relays and governing the output signal response.

Synthesis, growth, structure and spectroscopic characterization of a new organic nonlinear optical hydrogen bonding complex crystal: 3-carboxyl anilinium p-toluene sulfonate

A new organic nonlinear optical hydrogen bonding complex salt of 3-carboxyl anilinium p-toluene sulfonate has been synthesized and highly transparent good quality single crystals of it were successfully grown employing slow solvent evaporation solution growth technique at ambient temperature. The (1)H and (13)C NMR spectra were recorded to establish the molecular structure. The single crystal XRD analysis carried out reveals that the title salt crystallizes in monoclinic crystal system with non-centrosymmetric P2₁ space group. The FT-IR spectrum was recorded to confirm the presence of various functional groups in the grown title crystal. The UV-Vis-NIR transmission spectrum was recorded to apprehend the suitability of the single crystal of the title salt for various optical and NLO applications. The TG/DTA thermal analysis was performed to establish the thermal stability of the crystal. The SHG activity in the grown crystal was identified employing the modified Kurtz-Perry powder test. The electronic charge distribution and reactivity of the molecules within the title complex was studied by HOMO and LUMO analysis and the molecular electrostatic potential (MEP) of the title crystal was performed using the B3LYP method.

Synthesis, growth, spectral, and thermal studies of a new organic molecular charge transfer complex crystal: 3-nitroaniline 4-methyl benzene sulfonate

A new organic intermolecular charge transfer complex 3-nitroaniline 4-methyl benzene sulfonate (NATS) has been successfully synthesized and good optical quality single crystals grown by slow solvent evaporation solution growth technique at room temperature using methanol as the solvent. The (1)H and (13)C NMR spectra were recorded to establish the molecular structure of the title complex. The crystal structure of NATS has been determined by single crystal XRD analysis and it belongs to orthorhombic crystal system with space group Pbca. Fourier transform infrared (FT-IR) spectral study has been carried out to confirm the presence of various functional groups present in the complex. Electronic absorption spectrum was recorded to find the prevalent charge transfer activity in the complex. The UV-Vis-NIR transmission spectrum was recorded in the range 200-2500 nm, to find the optical transmittance window and lower cut off wavelength of the title crystal. The thermal stability of the title complex crystal was studied by using thermo-gravimetric and differential thermal analyses and found that the compound is stable up to 215 °C.

Synthesis, growth and spectroscopic investigation of an organic molecular charge transfer crystal: 8-hydroxy quinolinium 4-nitrobenzoate 4-nitrobenzoic acid

An organic intermolecular charge transfer complex salt of 8-Hydroxy quinolinium 4-nitrobenzoate 4-nitrobenzoic acid (OPNB) has been synthesized. Single crystals of OPNB were grown by slow solvent evaporation solution growth technique at room temperature. The (1)H and (13)C NMR spectra were recorded to confirm the molecular structure of the complex salt. The crystal structure of OPNB has been determined by single crystal XRD analysis and it belongs to triclinic crystal system with space group P-1. Fourier transform infrared (FT-IR) spectral study has been carried out to identify the various functional groups present. The UV-Vis-NIR transmittance spectrum was recorded in the range 200-2500nm, to find the suitability of the single crystal for various optical applications. The thermal stability of the crystal was investigated using thermogravimetric (TG) and differential thermal analyses (DTA).

Crystal growth, spectral, optical and thermal properties of semiorganic nonlinear optical material: picolinic acid hydrochloride

The bulk single crystal of 2-picolinic acid hydrochloride (PHCL) (a semi-organic nonlinear optical material of dimensions 25×15×10 mm(3)) was successfully grown by slow solvent evaporation technique. The XRD results revealed the cell parameters and the centrosymmetric nature of the crystal structure. FT-IR spectral study identified the functional groups, nature of bonding and their bond strength. The UV-Vis-NIR studies recognized the optical transmittance window and the lower cut off wavelength of the PHCL crystal and thus it could be performed as a NLO material. (1)H NMR and (13)CNMR spectra were correlated with the XRD standard for the molecular structure reveals harmony of the materials. Thermal properties of the crystal were studied by thermo gravimetric analysis (TGA) and differential thermal analysis (DTA); the derived kinetic parameter values support the intuitive association of picolinicacid and HCl leads to the spontaneous formation of PHCL with a first order reaction. The presence of a proton and a proton acceptor groups provide the necessary stability to induce charge asymmetry in the PHCL structure. The load dependent hardness values of the crystal were measured by microhardness testing.

Deterioration of coastal groundwater quality in Island and mainland regions of Ramanathapuram District, Southern India

A study was carried out in the Island and mainland regions of Ramanathapuram District to characterize the physico-chemical characteristics of 87 groundwater samples in Island and 112 groundwater samples in mainland which include pH, EC, TDS, salinity, total alkalinity, calcium hardness, magnesium hardness, total hardness, chloride and fluoride. Heavy inorganic load in majority of the groundwater samples has been estimated due to the salinity, TDS, TH and chloride beyond the threshold level which substantiates the percolation of sea water into the freshwater confined zones. Although the groundwater sources are available in plenty, the scarcity of potable water is most prevalent in this coastal area. The Water Quality Index (WQI) and Langeleir Saturation Index (LSI) have also been calculated to know the potable and corrosive/incrusting nature of the water samples. The statistical tools such as principal component analysis, box plots and correlation matrix have also been used to explain the influence of different physico-chemical parameters with respect to one another among the groundwater samples. The percentage of groundwater samples in mainland was more than that in Island with respect to the acceptable limit of WHO drinking standard, especially in TDS, CH, TH and chloride but the converse is observed in the case of fluoride. About 8% of the mainland aquifers and 42% of Island aquifers were identified to have fluoride greater than 1.5 mg/l. The signature of salt-water intrusion is observed from the ratio of Cl/CO(3)(2-) + HCO(3) and TA/TH. A proper management plan to cater potable water to the immediate needs of the people is to be envisaged.