Dual Inhibitors of Main Protease (MPro) and Cathepsin L as Potent Antivirals against SARS-CoV2.

Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.

Proximity-Dependent Labeling of Cysteines.

Mapping protein-protein interactions is crucial for understanding various signaling pathways in living cells, and developing new techniques for this purpose has attracted significant interest. Classic methods (e.g., the yeast two-hybrid) have been supplanted by more sophisticated chemical approaches that label proximal proteins (e.g., BioID, APEX). Herein we describe a proximity-based approach that uniquely labels cysteines. Our approach exploits the nicotinamide N-methyltransferase (NNMT)-catalyzed methylation of an alkyne-substituted 4-chloropyridine (SS6). Upon methylation of the pyridinium nitrogen, this latent electrophile diffuses out of the active site and labels proximal proteins on short time scales (≤5 min). We validated this approach by identifying known (and novel) interacting partners of protein arginine deiminase 2 (PAD2) and pyruvate dehydrogenase kinase 1 (PDK1). To our knowledge, this technology uniquely exploits a suicide substrate to label proximal cysteines in live cells.

Achieving water security in rural Indian Himalayas: A participatory account of challenges and potential solutions.

The complex and diverse factors that influence water security in the Indian Himalayan Region were examined using problem and solution tree (PAST) mapping together with a field study. Five PASTs, each constructed by a different group of stakeholders, namely the state government, the local government, researchers, development agencies, and the local community, were analysed to obtain a holistic and multi-sectoral understanding of water security in the region, and the analysis was supplemented with field data. The systematic study helped in (1) identifying many factors - climatic, geographical, cultural, and socio-economic - that influence water security, (2) assessing their impacts on mountain livelihoods, and (3) documenting thirty-two potential interventions in the form of adaptations (e.g. springshed management programme) and coping strategies (e.g. buying water from informal water markets) to strengthen water security. These strategies followed three main themes namely conserving water resources, improving rural livelihood and sustainable infrastructure development and risk management. The study also helped in building a shared sense of understanding, purpose, and action between the diverse groups of stakeholders. The study suggests that ensuring water security in rural mountain areas requires holistic and multi-sectoral policies, which should be developed by including all actors in the network of stakeholders; that local conditions be given utmost importance in the policy planning cycle (e.g. focus on springs in mountains); and that cultural landscape and local identities be closely examined to reduce the inequalities in access to resources.

Analyzing Social Networks to Examine the Changing Governance Structure of Springsheds: A Case Study of Sikkim in the Indian Himalayas.

The governance of natural resources now attracts greater participation of different stakeholders, ushering in a shift from conventional governance by the state to that by a network of stakeholders-a form of governance marked by a growing role of non-state and local actors. These changing dynamics are highlighted through a study of the governance network for springsheds in the Indian Himalayas by empirically mapping the changes in the Dhara Vikas Yojna, a plan or scheme (yojana) by the state for the development (vikas) of springs (dhara) in Sikkim, India, from policy planning to policy implementation. The study highlights the diverse existing and emerging roles of different stakeholders, the complex relationships between them, and the power dynamics that influence the management of springsheds. The study (1) identified some new but missing actors/actor groups that were critical to managing springs; (2) showed that although state governments continue to play a dominant role, decision making is shifting to non-state and local actors; and (3) highlighted the importance of exchanging knowledge and information in implementing a policy more effectively. Understanding the characteristics of the governance network helped in drawing lessons to make the plan more sustainable and replicable, which include considering the policy in the wider context of policies for other sectors such as sanitation and hydropower development, incentivising the emerging actors, and building a stronger interdisciplinary and inclusive knowledge network. Such an integrated approach to policymaking can also be adopted to analyze governance networks related to natural resources other than water.

Halogen Bonding Increases the Potency and Isozyme Selectivity of Protein Arginine Deiminase 1 Inhibitors.

Protein arginine deiminases (PADs) hydrolyze the side chain of arginine to form citrulline. Aberrant PAD activity is associated with rheumatoid arthritis, multiple sclerosis, lupus, and certain cancers. These pathologies established the PADs as therapeutic targets and multiple PAD inhibitors are known. Herein, we describe the first highly potent PAD1-selective inhibitors (1 and 19). Detailed structure-activity relationships indicate that their potency and selectivity is due to the formation of a halogen bond with PAD1. Importantly, these inhibitors inhibit histone H3 citrullination in HEK293TPAD1 cells and mouse zygotes with excellent potency. Based on this scaffold, we also developed a PAD1-selective activity-based probe that shows remarkable cellular efficacy and proteome selectivity. Based on their potency and selectivity we expect that 1 and 19 will be widely used chemical tools to understand PAD1 biology.

Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines.

Experimental measurement of the contribution of H-bonding to intermolecular and intramolecular interactions that provide specificity to biological complex formation is an important aspect of macromolecular chemistry and structural biology. However, there are very few viable methods available to determine the energetic contribution of an individual hydrogen bond to binding and catalysis in biological systems. Therefore, the methods that use secondary deuterium isotope effects analyzed by NMR or equilibrium or kinetic isotope effect measurements are attractive ways to gain information on the H-bonding properties of an alcohol system, particularly in a biological environment. Here, we explore the anharmonic contribution to the C-H group when the O-H group of 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) forms an intermolecular H-bond with the amines by quantum mechanical calculations and by experimentally measuring the H/D effect by NMR. Within the framework of density functional theory, ab initio calculations were carried out for HFP in its two different conformational states and their H-bonded complexes with tertiary amines to determine the (13)C chemical shielding, change in their vibrational equilibrium distances, and the deuterium isotope effect on (13)C2 (secondary carbon) of HFP upon formation of complexes with tertiary amines. When C2-OH was involved in hydrogen bond formation (O-H as hydrogen donor), it weakened the geminal C2-H bond; it was reflected in the NMR chemical shift, coupling constant, and the equilibrium distances of the C-H bond. The first derivative of nuclear shielding at C2 in HFP was -48.94 and -50.73 ppm Å(-1) for anti and gauche conformations, respectively. In the complex, the values were -50.28 and -50.76 ppm Å(-1), respectively. The C-H stretching frequency was lower than the free monomer, indicating enhanced anharmonicity in the C-H bond in the complex form. In chloroform, HFP formed a complex with the amine; δC2 was 69.107 ppm for HFP-triethylamine and 68.766 ppm for HFP-d2-triethylamine and the difference in chemical shift, the ΔδC2 was 341 ppb. The enhanced anharmonicity in the hydrogen-bonded complex resulted in a larger vibrational equilibrium distance in C-H/D bonds. An analysis with the Morse potential function indicated that the enhanced anharmonicity encountered in the bond was the origin of a larger isotope effect and the equilibrium distances. Change in vibrational equilibrium distance and the deuterium isotope effect, as observed in the complex, could be used as parameters in monitoring the strength of the H-bond in small model systems with promising application in biomacromolecules.

Typology of Battery Cells - From Liquid to Solid Electrolytes.

The field of battery research is bustling with activity and the plethora of names for batteries that present new cell concepts is indicative of this. Most names have grown historically, each indicative of the research focus in their own time, e.g. lithium-ion batteries, lithium-air batteries, solid-state batteries. Nevertheless, all batteries are essentially made of two electrode layers and an electrolyte layer. This lends itself to a systematic and comprehensive approach by which to identify the cell type and chemistry at a glance. The recent increase in hybridized cell concepts potentially opens a world of new battery types. To retain an overview of this dynamic research field, each battery type is briefly discussed and a systematic typology of battery cells is proposed in the form of the short and universal cell naming system AAM XEBCAM (AAM: anode active material; X: L (liquid), G (gel), PP (plasticized polymer), DP (dry polymer), S (solid), H (hybrid); EB: electrolyte battery; CAM: cathode active material). This classification is based on the principal ion conduction mechanism of the electrolyte during cell operation. Even though the presented typology initiates from the research fields of lithium-ion, solid-state and hybrid battery concepts, it is applicable to any battery cell chemistry.

Site-specific incorporation of citrulline into proteins in mammalian cells.

Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination.

Time-Temperature Scaling and Dielectric Modeling of Conductivity Spectra of Single-Ion Conducting Liquid Dendrimer Electrolytes.

We discuss here the time-temperature scaling and dielectric modeling of the variation of single-ion conductivity with frequency of first generation (G1) liquid dendrimer electrolyte, viz., Poly(propyl ether imine) (PETIM):Li-salt. The PETIM:Li-salt electrolyte exhibits a cation/anion transference number close to unity in the liquid state. On switching from an ester (G1-COOR) to cyano (G1-CN) peripheral group, keeping constant the linker (ether) and branching groups (amine), an interesting transformation from cationic ( t+ ∼1) to anionic conductor ( t- ∼1) takes place. The switch in the nature of the predominant charge carrier is directly related to the change in the magnitude of anion diffusion ( D-), which increases by 1 order of magnitude from D- = 1.1 × 10-12 m2 s-1 (at 30 °C) in G1-COOR to D- = 1.3 × 10-11 m2 s-1 (at 30 °C) in G1-CN. This intriguing ion transport mechanism is probed comprehensively using ac-impedance spectroscopy. The frequency dependent ionic conductivity of G1-CN/G1-COOR, comprised of distinct frequency regimes, is analyzed using the time-temperature superposition scaling principle (TTSP) based on Summerfield and Baranovski scaling methods. To gain insight into the electrical polarization (EP) phenomenon, the relevant frequency regime is converted from conductivity to dielectric versus frequency. The dielectric versus frequency data is modeled using Macdonald and Coelho. The combined approach of TTSP and dielectric modeling provide explicitly the extent of the influence of ion-dendrimer, ion-ion interactions, and also the mobile charge carrier density on the effective ion transport in the homogeneous single-ion conducting dendrimer electrolytes. The combined analysis suggests that ion transport in PETIM-COOR is only due to enhanced ion mobility, whereas in PETIM-CN it is due to both mobile charge carrier concentration and ion mobility. To the best of our knowledge, the scaling and modeling approaches employed here constitute a rare example for validation of such concepts in the context of dendrimer electrolytes.

Development of a Suicide Inhibition-Based Protein Labeling Strategy for Nicotinamide N-Methyltransferase.

Nicotinamide N-methyltransferase (NNMT) catalyzes the S-adenosyl-l-methionine-dependent methylation of nicotinamide to form N-methylnicotinamide. This enzyme detoxifies xenobiotics and regulates NAD+ biosynthesis. Additionally, NNMT is overexpressed in various cancers. Herein, we describe the first NNMT-targeted suicide substrates. These compounds, which include 4-chloropyridine and 4-chloronicotinamide, exploit the broad substrate scope of NNMT; methylation of the pyridine nitrogen enhances the electrophilicity of the C4 position, thereby promoting an aromatic nucleophilic substitution by C159, a noncatalytic cysteine. On the basis of this activity, we developed a suicide inhibition-based protein labeling strategy using an alkyne-substituted 4-chloropyridine that selectively labels NNMT in vitro and in cells. In total, this study describes the first NNMT-directed activity-based probes.

Ion Transport Mechanism of a Gel Electrolyte Comprising a Salt in Binary Plastic Crystalline Mixtures Confined inside a Polymer Network.

We discuss here the ion transport mechanism of a gel electrolyte comprising lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) solvated by two plastic crystalline solvents, one a solid (succinonitrile, abbreviated as SN) and another (a room temperature ionic liquid) (1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide, (abbreviated as IL) confined inside a linear network of poly(methyl methacrylate) (PMMA). The concentration of the IL component (x) determines the physical properties of the unconfined electrolyte (i.e., SN1-xILx-LiTFSI) and when confined inside the polymer network (GPE-x). The extent of disorder in the SN1-xILx-LiTFSI and the GPE-x electrolytes is enhanced compared to both the bare SN-LiTFSI and IL-LiTFSI electrolytes. The enhanced disordering in the plastic phase alters both the local ion environment and viscosity. These changes strongly influence the ion mobility and nature of predominant charge carriers and thus the ion conduction mechanism in SN1-xILx-LiTFSI and GPE-x. The proposed SN1-xILx-LiTFSI and the GPE-x electrolytes show predominantly anion conduction (tTFSI ≈ 0.5); however, lithium transference number (tLi ≈ 0.2) is nearly an order higher than the IL-LiTFSI (tLi ≈ 0.02-0.06). The ionic conductivity of SN1-xILx-LiTFSI is much higher (especially for x ≈ 0.1) compared to both SN-LiTFSI and IL-LiTFSI. The ionic conductivity of the GPE-x, though lower than the unconfined SN1-xILx-LiTFSI electrolytes, is still very promising, displaying values of ∼10-3 Ω-1 cm-1. The GPE-x displayed compliable mechanical properties, stable Li-electrode/electrolyte interface, low rate of Al corrosion, and stable cyclability over several tens of charge-discharge cycles when assembled in a separator-free Li-graphite cell. The promising electrochemical performance further justifies the simple strategy of employing mixed physical state plasticizers to tune the physical properties of polymer electrolytes requisite for application in rechargeable batteries.

A single cation or anion dendrimer-based liquid electrolyte.

We propose here a novel liquid dendrimer-based single ion conductor as a potential alternative to conventional molecular liquid solvent-salt solutions in rechargeable batteries, sensors and actuators. A specific change from ester (-COOR) to cyano (-CN) terminated peripheral groups in generation-one poly(propyl ether imine) (G1-PETIM)-lithium salt complexes results in a remarkable switchover from a high cation (tLi+ = 0.9 for -COOR) to a high anion (tPF6- = 0.8 for -CN) transference number. This observed switchover draws an interesting analogy with the concept of heterogeneous doping, applied successfully to account for similar changes in ionic conductivity arising out of dispersion of insulator particle inclusions in weak inorganic solid electrolytes. The change in peripheral group simultaneously affects the effective ionic conductivity, with the room temperature ionic conductivity of PETIM-CN (1.9 × 10-5 Ω-1 cm-1) being an order of magnitude higher than PETIM-COOR (1.9 × 10-6 Ω-1 cm-1). Notably, no significant changes are observed in the lithium mobility even following changes in viscosity due to the change in the peripheral group. Changes in the peripheral chemical functionality directly influence the anion mobility, being lower in PETIM-COOR than in PETIM-CN, which ultimately becomes the sole parameter controlling the effective transport and electrochemical properties of the dendrimer electrolytes.

Silver-catalysed azide-alkyne cycloaddition (AgAAC): assessing the mechanism by density functional theory calculations.

'Click reactions' are the copper catalysed dipolar cycloaddition reaction of azides and alkynes to incorporate nitrogens into a cyclic hydrocarbon scaffold forming a triazole ring. Owing to its efficiency and versatility, this reaction and the products, triazole-containing heterocycles, have immense importance in medicinal chemistry. Copper is the only known catalyst to carry out this reaction, the mechanism of which remains unclear. We report here that the 'click reactions' can also be catalysed by silver halides in non-aqueous medium. It constitutes an alternative to the well-known CuAAC click reaction. The yield of the reaction varies on the type of counter ion present in the silver salt. This reaction exhibits significant features, such as high regioselectivity, mild reaction conditions, easy availability of substrates and reasonably good yields. In this communication, the findings of a new catalyst along with the effect of solvent and counter ions will help to decipher the still obscure mechanism of this important reaction.

pKa determination of D-ribose by Raman spectroscopy.

Determination of the pKa of OH groups present in D-ribose is crucial in order to elucidate the origin and mechanism of many catalytic processes that involve the ribose unit. However, there is hardly any reports about the experimental pKa of the OH group due to the lack of an appropriate method. In this study we investigated the protonation state of OH groups in D-ribose by introducing C-D labeling and measuring the changes in the isolated C-D frequency in several isotopologues of the compound with pH. The large shift in the νC-D of D-ribose-C1-D in ionized condition compared to other deuterium-substituted D-riboses (e.g., D-ribose-C2-D, D-ribose-C3-D, etc.) confirmed that the C1-OH group preferred ionization, and the ionization pKa was 11.8. Both the ionized and the unionized structures of D-ribose preferred the pyranose conformation, which was supported by (13)C NMR experiments. Electronic redistribution via resonance and intramolecular hydrogen-bond formation were proposed to account for the stabilization of the ionized structure.

Excellent performance of few-layer borocarbonitrides as anode materials in lithium-ion batteries.

Borocarbonitrides (BxCyNz) with a graphene-like structure exhibit a remarkable high lithium cyclability and current rate capability. The electrochemical performance of the Bx Cy Nz materials, synthesized by using a simple solid-state synthesis route based on urea, was strongly dependent on the composition and surface area. Among the three compositions studied, the carbon-rich compound B0.15C0.73N0.12 with the highest surface area showed an exceptional stability (over 100 cycles) and rate capability over widely varying current density values (0.05-1 A g(-1)). B0.15C0.73N0.12 has a very high specific capacity of 710 mA h g(-1) at 0.05 A g(-1) . With the inclusion of a suitable additive in the electrolyte, the specific capacity improved drastically, recording an impressive value of nearly 900 mA h g(-1) at 0.05 A g(-1) . It is believed that the solid-electrolyte interphase (SEI) layer at the interface of BxCyNz and electrolyte also plays a crucial role in the performance of the BxCyNz .