DAIKON: A Data Acquisition, Integration, and Knowledge Capture Web Application for Target-Based Drug Discovery.

Primitive data organization practices struggle to deliver at the scale and consistency required to meet multidisciplinary collaborations in drug discovery. For effective data sharing and coordination, a unified platform that can collect and analyze scientific information is essential. We present DAIKON, an open-source framework that integrates targets, screens, hits, and manages projects within a target-based drug discovery portfolio. Its knowledge capture components enable teams to record subsequent molecules as their properties improve, facilitate team collaboration through discussion threads, and include modules that visually illustrate the progress of each target as it advances through the pipeline. It serves as a repository for scientists sourcing data from Mycobrowser, UniProt, PDB. The goal is to globalize several variations of the drug-discovery program without compromising local aspects of specific workflows. DAIKON is modularized by abstracting the database and creating separate layers for entities, business logic, infrastructure, APIs, and frontend, with each tier allowing for extensions. Using Docker, the framework is packaged into two solutions: daikon-server-core and daikon-client. Organizations may deploy the project to on-premises servers or VPC. Active-Directory/SSO is supported for user administration. End users can access the application with a web browser. Currently, DAIKON is implemented in the TB Drug Accelerator program (TBDA).

Histidine phosphorylation relieves copper inhibition in the mammalian potassium channel KCa3.1.

KCa2.1, KCa2.2, KCa2.3 and KCa3.1 constitute a family of mammalian small- to intermediate-conductance potassium channels that are activated by calcium-calmodulin. KCa3.1 is unique among these four channels in that activation requires, in addition to calcium, phosphorylation of a single histidine residue (His358) in the cytoplasmic region, by nucleoside diphosphate kinase-B (NDPK-B). The mechanism by which KCa3.1 is activated by histidine phosphorylation is unknown. Histidine phosphorylation is well characterized in prokaryotes but poorly understood in eukaryotes. Here, we demonstrate that phosphorylation of His358 activates KCa3.1 by antagonizing copper-mediated inhibition of the channel. Furthermore, we show that activated CD4(+) T cells deficient in intracellular copper exhibit increased KCa3.1 histidine phosphorylation and channel activity, leading to increased calcium flux and cytokine production. These findings reveal a novel regulatory mechanism for a mammalian potassium channel and for T-cell activation, and highlight a unique feature of histidine versus serine/threonine and tyrosine as a regulatory phosphorylation site.

Identification of PGAM5 as a Mammalian Protein Histidine Phosphatase that Plays a Central Role to Negatively Regulate CD4(+) T Cells.

Whereas phosphorylation of serine, threonine, and tyrosine is exceedingly well characterized, the role of histidine phosphorylation in mammalian signaling is largely unexplored. Here we show that phosphoglycerate mutase family 5 (PGAM5) functions as a phosphohistidine phosphatase that specifically associates with and dephosphorylates the catalytic histidine on nucleoside diphosphate kinase B (NDPK-B). By dephosphorylating NDPK-B, PGAM5 negatively regulates CD4(+) T cells by inhibiting NDPK-B-mediated histidine phosphorylation and activation of the K(+) channel KCa3.1, which is required for TCR-stimulated Ca(2+) influx and cytokine production. Using recently developed monoclonal antibodies that specifically recognize phosphorylation of nitrogens at the N1 (1-pHis) or N3 (3-pHis) positions of the imidazole ring, we detect for the first time phosphoisoform-specific regulation of histidine-phosphorylated proteins in vivo, and we link these modifications to TCR signaling. These results represent an important step forward in studying the role of histidine phosphorylation in mammalian biology and disease.

Natural antibodies bridge innate and adaptive immunity.

Natural Abs, belonging to isotypes IgM, IgG3, and IgA, were discovered nearly half a century ago. Despite knowledge about the role of the polyreactive natural IgM in pathogen elimination, B cell survival and homeostasis, inflammatory diseases, and autoimmunity, there is a lack of clarity about the physiological role of natural IgG and natural IgA because they appear incapable of recognizing Ags on their own and are perceived as nonreactive. However, recent research revealed exciting functions of natural IgG in innate immunity. Natural IgG:lectin collaboration swiftly and effectively kills invading pathogens. These advances prompt further examination of natural Abs in immune defense and homeostasis, with the potential for developing novel therapeutics. This review provides new insights into the interaction between natural Abs and lectins, with implications on how interactions between molecules of the innate and adaptive immune systems bridge these two arms of immunity.

Molecular interaction between natural IgG and ficolin--mechanistic insights on adaptive-innate immune crosstalk.

Recently, we found that natural IgG (nIgG; a non-specific immunoglobulin of adaptive immunity) is not quiescent, but plays a crucial role in immediate immune defense by collaborating with ficolin (an innate immune protein). However, how the nIgG and ficolin interplay and what factors control the complex formation during infection is unknown. Here, we found that mild acidosis and hypocalcaemia induced by infection- inflammation condition increased the nIgG:ficolin complex formation. Hydrogen-deuterium exchange mass spectrometry delineated the binding interfaces to the CH2-CH3 region of nIgG Fc and P-subdomain of ficolin FBG domain. Infection condition exposes novel binding sites. Site-directed mutagenesis and surface plasmon resonance analyses of peptides, derived from nIgG and ficolin, defined the interacting residues between the proteins. These results provide mechanistic insights on the interaction between two molecules representing the adaptive and innate immune pathways, prompting potential development of immunomodulatory/prophylactic peptides tunable to prevailing infection conditions.

Natural IgG antibodies provide innate protection against ficolin-opsonized bacteria.

For nearly five decades since its discovery, the role of natural IgG, which pre-exists in neonates and uninfected individuals, has remained unclear due to the general perception that natural antibodies lack affinity for pathogens. Here, we show for the first time that natural IgG recognizes a spectrum of bacteria through lectins like ficolin and mannose binding lectin (MBL). Infection-inflammation condition markedly increased the affinity of natural IgG for bacteria associated with ficolins. After opsonization with IgG:ficolin complex, the bacteria were phagocytosed by monocytes via FcγRI. Infection of C3(-/-) mice indicated that the natural IgG-mediated immune complex was formed independently of C3. AID(-/-) mice lacking IgG were susceptible to infection, unless reconstituted with natural IgG. Thus, we have proven that natural IgG is not quiescent; rather, it plays a vital and immediate role in immune defense. Our findings provide a fresh perspective on natural antibodies, opening new avenues to explore host-microbe interaction.

The effect of band Jahn-Teller distortion on the magnetoresistivity of manganites: a model study.

We present a model study of magnetoresistance through the interplay of magnetisation, structural distortion and external magnetic field for the manganite systems. The manganite system is described by the Hamiltonian which consists of the s-d type double exchange interaction, Heisenberg spin-spin interaction among the core electrons, and the static and dynamic band Jahn-Teller (JT) interaction in the e(g) band. The relaxation time of the e(g) electron is found from the imaginary part of the Green's function using the total Hamiltonian consisting of the interactions due to the electron and phonon. The calculated resistivity exhibits a peak in the pure JT distorted insulating phase separating the low temperature metallic ferromagnetic phase and the high temperature paramagnetic phase. The resistivity is suppressed with the increase of the external magnetic field. The e(g) electron band splitting and its effect on magnetoresistivity is reported here.

Theoretical study of the Raman active CDW gap mode in manganites.

We report here the microscopic theory of the Raman spectra of the colossal magnetoresistive (CMR) manganite systems. The system is described by a model Hamiltonian consisting of the double exchange interaction in addition to the charge ordering interaction in the e(g) band and spin-spin interaction among the t(2g) core electrons. Further the phonon coupling to the conduction electron density is incorporated in the model for phonons in the harmonic approximation. The spectral density function for the Raman spectra is calculated from the imaginary part of the phonon Green's function. The calculated spectra display the Raman active bare phonon peak along with the charge ordering peak. The magnetic field and temperature dependence of the charge ordering peak agrees with the 480 cm(-1) JT mode observed in the experiments. The evolution of this mode is investigated in the report.