Calcium-dependent association of calmodulin with the rubella virus nonstructural protease domain

Identification of a potential anti-viral drug targeting allosteric site of papain-like protease against rubella using a molecular modeling approach

Rubella virus (RUBV) is responsible for causing rashes, lymphadenopathy, and fever which are the hallmarks of an acute viral illness called Rubella. For RUBV replication, the non-structural polyprotein p200 must be cleaved by the rubella papain-like protease (RubPro) into the multifunctional proteins p150 and p90. Hence, RubPro is an attractive target for anti-viral drug discovery. Moreover, the binding of host Calmodulin 1 (CaM) to RubPro modulates the protease activity and infectivity of RUBV. However, the binding mode of CaM and RubPro remain uncertain. Therefore, our investigation not only delves into understanding the interaction between CaM and the RubPro but also aims to recognize the allosteric site for the development of antiviral protease inhibitors. In this study, we interestingly identified the allosteric site in close vicinity with the CaM binding domain of RubPro. Considering the allosteric site of RubPro, we employed a computational modelling approach to identify the potential antiviral compounds. Leveraging ChemDiv protease inhibitors database, we employed structure-based virtual screening, ADME, pass prediction, and docking studies, unveiling three potent compounds: C073-2897, C073-3328, and C073-3368. Moreover, molecular dynamics simulation analysis revealed that these compounds affect the RubPro structure and dynamics and may also influence the binding of CaM with RubPro. Notably, binding energy calculation showed that the compound C073-3328 exhibits higher binding affinity, while C073-3368 displays a lower binding affinity with RubPro. These compounds signify potential for managing RUBV infections and pioneering effective antiviral treatments. This computational study could pave the way for improved methods of managing or controlling rubella infections.

Crystal structure of the Rubella virus protease reveals a unique papain-like protease fold

Rubella, a viral disease characterized by a red skin rash, is well controlled because of an effective vaccine, but outbreaks are still occurring in the absence of available antiviral treatments. The Rubella virus (RUBV) papain-like protease (RubPro) is crucial for RUBV replication, cleaving the nonstructural polyprotein p200 into two multifunctional proteins, p150 and p90. This protease could represent a potential drug target, but structural and mechanistic details important for the inhibition of this enzyme are unclear. Here, we report a novel crystal structure of RubPro at a resolution of 1.64 Å. The RubPro adopts a unique papain-like protease fold, with a similar catalytic core to that of proteases from Severe acute respiratory syndrome coronavirus 2 and foot-and-mouth disease virus while having a distinctive N-terminal fingers domain. RubPro has well-conserved sequence motifs that are also found in its newly discovered Rubivirus relatives. In addition, we show that the RubPro construct has protease activity in trans against a construct of RUBV protease-helicase and fluorogenic peptides. A protease-helicase construct, exogenously expressed in Escherichia coli, was also cleaved at the p150-p90 cleavage junction, demonstrating protease activity of the protease-helicase protein. We also demonstrate that RubPro possesses deubiquitylation activity, suggesting a potential role of RubPro in modulating the host's innate immune responses. We anticipate that these structural and functional insights of RubPro will advance our current understanding of its function and help facilitate more structure-based research into the RUBV replication machinery, in hopes of developing antiviral therapeutics against RUBV.

Implications of TORCH Diseases in Retinal Development-Special Focus on Congenital Toxoplasmosis

There are certain critical periods during pregnancy when the fetus is at high risk for exposure to teratogens. Some microorganisms, including Toxoplasma gondii, are known to exhibit teratogenic effects, interfering with fetal development and causing irreversible disturbances. T. gondii is an obligate intracellular parasite and the etiological agent of Toxoplasmosis, a zoonosis that affects one third of the world's population. Although congenital infection can cause severe fetal damage, the injury extension depends on the gestational period of infection, among other factors, like parasite genotype and host immunity. This parasite invades the Central Nervous System (CNS), forming tissue cysts, and can interfere with neurodevelopment, leading to frequent neurological abnormalities associated with T. gondii infection. Therefore, T. gondii is included in the TORCH complex of infectious diseases that may lead to neurological malformations (Toxoplasmosis, Others, Rubella, Cytomegalovirus, and Herpes). The retina is part of CNS, as it is derived from the diencephalon. Except for astrocytes and microglia, retinal cells originate from multipotent neural progenitors. After cell cycle exit, cells migrate to specific layers, undergo morphological and neurochemical differentiation, form synapses and establish their circuits. The retina is organized in nuclear layers intercalated by plexus, responsible for translating and preprocessing light stimuli and for sending this information to the brain visual nuclei for image perception. Ocular toxoplasmosis (OT) is a very debilitating condition and may present high severity in areas in which virulent strains are found. However, little is known about the effect of congenital infection on the biology of retinal progenitors/ immature cells and how this infection may affect the development of this tissue. In this context, this study reviews the effects that congenital infections may cause to the developing retina and the cellular and molecular aspects of these diseases, with special focus on congenital OT.

Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions

Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe) joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines) several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be explained as modulation of a pre-existing dynamic equilibrium between different conformations of calmodulin's lobes, in agreement with linkage theory and MWC-type models.

A fluorogenic peptide probe developed by in vitro selection using tRNA carrying a fluorogenic amino acid

A peptide that binds and emits fluorescence in response to conformational change in a target protein was developed by in vitro selection using tRNA carrying a fluorogenic amino acid. This technology could prove to be useful for the development of separation-free immunoassays and bio-imaging analyses.

Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems

Calcium ion (Ca(2+)), the fifth most common chemical element in the earth's crust, represents the most abundant mineral in the human body. By binding to a myriad of proteins distributed in different cellular organelles, Ca(2+) impacts nearly every aspect of cellular life. In prokaryotes, Ca(2+) plays an important role in bacterial movement, chemotaxis, survival reactions and sporulation. In eukaryotes, Ca(2+) has been chosen through evolution to function as a universal and versatile intracellular signal. Viruses, as obligate intracellular parasites, also develop smart strategies to manipulate the host Ca(2+) signaling machinery to benefit their own life cycles. This review focuses on recent advances in applying both bioinformatic and experimental approaches to predict and validate Ca(2+)-binding proteins and their interactomes in biological systems on a genome-wide scale (termed "calciomics"). Calmodulin is used as an example of Ca(2+)-binding protein (CaBP) to demonstrate the role of CaBPs on the regulation of biological functions. This review is anticipated to rekindle interest in investigating Ca(2+)-binding proteins and Ca(2+)-modulated functions at the systems level in the post-genomic era.