Towards superior mRNA caps accessible by click chemistry: synthesis and translational properties of triazole-bearing oligonucleotide cap analogs

Messenger RNA (mRNA)-based gene delivery is a powerful strategy for the development of vaccines and therapeutics. Consequently, approaches that enable efficient synthesis of mRNAs with high purity and biological activity are in demand. Chemically modified 7-methylguanosine (m⁷G) 5' caps can augment the translational properties of mRNA; however, efficient synthesis of structurally complex caps, especially on a large scale, is challenging. Previously, we proposed a new strategy to assemble dinucleotide mRNA caps by replacing the traditional pyrophosphate bond formation by copper-catalyzed azide-alkyne cycloaddition (CuAAC). Here, we used CuAAC to synthesize 12 novel triazole-containing tri- and tetranucleotide cap analogs with the aim of exploring the chemical space around the first transcribed nucleotide in mRNA and overcoming some of the limitations previously reported for the triazole-containing dinucleotide analogs. We evaluated the efficiency of incorporation into RNA for these analogs and their influence on the translational properties of in vitro transcribed (IVT) mRNAs in rabbit reticulocyte lysate and JAWS II cultured cells. The incorporation of the triazole moiety within the 5',5'-oligophosphate of trinucleotide cap produced compounds that were well incorporated into RNA by T7 polymerase while replacing the 5',3'-phosphodiester bond with triazole impaired incorporation and translation efficiency, despite a neutral effect on the interaction with the translation initiation factor eIF4E. One of the compounds (m⁷Gppp-tr-C₂H₄pA_mpG), had translational activity and other biochemical properties comparable to natural cap 1 structure, thus being a promising mRNA capping reagent for potential in cellulo and in vivo applications in the field of mRNA-based therapeutics.

Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism

Cytosolic nucleotidases (cNs) catalyze dephosphorylation of nucleoside 5’-monophosphates and thereby contribute to the regulation of nucleotide levels in cells. cNs have also been shown to dephosphorylate several therapeutically relevant nucleotide analogues. cN-IIIB has shown in vitro a distinctive activity towards 7-mehtylguanosine monophosphate (m⁷GMP), which is one key metabolites of mRNA cap. Consequently, it has been proposed that cN-IIIB participates in mRNA cap turnover and prevents undesired accumulation and salvage of m⁷GMP. Here, we sought to develop molecular tools enabling more advanced studies on the cellular role of cN-IIIB. To that end, we performed substrate and inhibitor property profiling using a library of 41 substrate analogs. The most potent hit compounds (identified among m⁷GMP analogs) were used as a starting point for structure–activity relationship studies. As a result, we identified several 7-benzylguanosine 5’-monophosphate (Bn⁷GMP) derivatives as potent, unhydrolyzable cN-IIIB inhibitors. The mechanism of inhibition was elucidated using X-ray crystallography and molecular docking. Finally, we showed that compounds that potently inhibit recombinant cN-IIIB have the ability to inhibit m⁷GMP decay in cell lysates.

A Hybrid (Numerical-physical) Model of the Left Ventricle

Hydraulic models of the circulation are used to test mechanical devices and for training and research purposes; when compared to numerical models, however, they are not flexible enough and rather expensive. The solution proposed here is to merge the characteristics and the flexibility of numerical models with the functions of physical models. The result is a hybrid model with numerical and physical sections connected by an electro-hydraulic interface - which is to some extent the main problem since the numerical model can be easily changed or modified.

The concept of hybrid model is applied to the representation of ventricular function by a variable elastance numerical model. This prototype is an open loop circuit and the physical section is built out of a reservoir (atrium) and a modified windkessel (arterial tree). The corresponding equations are solved numerically using the variables (atrial and arterial pressures) coming from the physical circuit. Ventricular output flow is the computed variable and is sent to a servo amplifier connected to a DC motor-gear pump system. The gear pump, behaving roughly as a flow source, is the interface to the physical circuit. Results obtained under different hemodynamic conditions demonstrate the behaviour of the ventricular model on the pressure-volume plane and the time course of output flow and arterial pressure.

Application of a user-friendly comprehensive circulatory model for estimation of hemodynamic and ventricular variables

Purpose

Application of a comprehensive, user-friendly, digital computer circulatory model to estimate hemodynamic and ventricular variables.

Methods

The closed-loop lumped parameter circulatory model represents the circulation at the level of large vessels. A variable elastance model reproduces ventricular ejection. The circulatory model has been modified embedding an algorithm able to adjust the model parameters reproducing specific circulatory conditions. The algorithm reads input variables: heart rate, aortic pressure, cardiac output, and left atrial pressure. After a preliminary estimate of circulatory parameters and ventricular elastance, it adjusts the amount of circulating blood, the value of the systemic peripheral resistance, left ventricular elastance, and ventricular rest volume. Input variables and the corresponding calculated variables are recursively compared: the procedure is stopped if the difference between input and calculated variables is within the set tolerance. At the procedure end, the model produces an estimate of ventricular volumes and Emaxl along with systemic and pulmonary pressures (output variables). The procedure has been tested using 4 sets of experimental data including left ventricular assist device assistance.

Results

The algorithm allows the reproduction of the circulatory conditions defined by all input variable sets, giving as well an estimate of output variables.

Conclusions

The algorithm permits application of the model in environments where the simplicity of use and velocity of execution are of primary importance. Due to its modular structure, the model can be modified adding new circulatory districts or changing the existing ones. The model could also be applied in educational applications.

Modelling of Cardiovascular System: Development of a Hybrid (Numerical-Physical) Model

Physical models of the circulation are used for research, training and for testing of implantable active and passive circulatory prosthetic and assistance devices. However, in comparison with numerical models, they are rigid and expensive. To overcome these limitations, we have developed a model of the circulation based on the merging of a lumped parameter physical model into a numerical one (producing therefore a hybrid). The physical model is limited to the barest essentials and, in this application, developed to test the principle, it is a windkessel representing the systemic arterial tree. The lumped parameters numerical model was developed in LabVIEW environment and represents pulmonary and systemic circulation (except the systemic arterial tree). Based on the equivalence between hydraulic and electrical circuits, this prototype was developed connecting the numerical model to an electrical circuit--the physical model. This specific solution is valid mainly educationally but permits the development of software and the verification of preliminary results without using cumbersome hydraulic circuits. The interfaces between numerical and electrical circuits are set up by a voltage controlled current generator and a voltage controlled voltage generator. The behavior of the model is analyzed based on the ventricular pressure-volume loops and on the time course of arterial and ventricular pressures and flow in different circulatory conditions. The model can represent hemodynamic relationships in different ventricular and circulatory conditions.

7-Methylguanosine monophosphate analogues with 5'-(1,2,3-triazoyl) moiety: Synthesis and evaluation as the inhibitors of cNIIIB nucleotidase

The hydrolysis of nucleoside 5'-monophosphates to the corresponding nucleosides and inorganic phosphate is catalysed by 5'-nucleotidases, thereby contributing to the control of endogenous nucleotide turnover and affecting the fate of exogenously delivered nucleotide- and nucleoside-derived therapeutics in cells. A recently identified nucleotidase cNIIIB shows preference towards 7-methylguanosine monophosphate (m⁷GMP) as a substrate, which suggests its potential involvement in mRNA degradation. However, the extent of biological functions and the significance of cNIIIB remains to be elucidated. Here, we synthesised a series of m⁷GMP analogues carrying a 1,2,3-triazole moiety at the 5' position as the potential inhibitors of human cNIIIB. The compounds were synthesised by using the copper-catalysed azide-alkyne cycloaddition (CuAAC) between 5'-azido-5'-deoxy-7-methylguanosine and different phosphate or phosphonate derivatives carrying terminal alkyne. The analogues were evaluated as cNIIIB inhibitors using HPLC and malachite green assays, demonstrating that compound 1a, carrying a 1,2,3-triazoylphosphonate moiety, inhibits cNIIIB activity at micromolar concentrations (IC₅₀ 87.8 ± 7.5 µM), while other analogues showed no activity. In addition, compound 1d was identified as an artifical substrate for ^HscNIIIB. Further characterization of inhibitor 1a revealed that it is poorly recognised by other m⁷G-binding proteins, eIF4E and DcpS, indicating its selectivity towards cNIIIB. The first inhibitor (1a) and unnatural substrate (1d) of cNIIIB, identified here, can be used as molecular probes for the elucidation of biological roles of cNIIIB, including the verification of its proposed function in mRNA metabolism.

Experimental integration of Autoregulation Unit for left ventricular assist devices in a cardiovascular hybrid simulator

In this paper, an Autoregulation Unit (ARU) for left ventricular sensorized assist devices (LVAD) has been used with a cardiovascular hybrid simulator mimicking physiological and pathological patient conditions. The functionalities of the ARU have been demonstrating for the successful receiving and visualization of system parameters, sending of commands for LVAD speed changes, and enabling of the autonomous flow control algorithm. Experiments of speed changes and autoregulation are reported, showing the feasibility of the approach for both local and remote control of a LVAD.

Development of a hybrid (numerical-hydraulic) circulatory model: prototype testing and its response to IABP assistance

Merging numerical and physical models of the circulation makes it possible to develop a new class of circulatory models defined as hybrid. This solution reduces the costs, enhances the flexibility and opens the way to many applications ranging from research to education and heart assist devices testing. In the prototype described in this paper, a hydraulic model of systemic arterial tree is connected to a lumped parameters numerical model including pulmonary circulation and the remaining parts of systemic circulation. The hydraulic model consists of a characteristic resistance, of a silicon rubber tube to allow the insertion of an Intra-Aortic Balloon Pump (IABP) and of a lumped parameters compliance. Two electro-hydraulic interfaces, realized by means of gear pumps driven by DC motors, connect the numerical section with both terminals of the hydraulic section. The lumped parameters numerical model and the control system (including analog to digital and digital to analog converters)are developed in LabVIEW environment. The behavior of the model is analyzed by means of the ventricular pressure-volume loops and the time courses of arterial and ventricular pressures and flows in different circulatory conditions. A simulated pathological condition was set to test the IABP and verify the response of the system to this type of mechanical circulatory assistance. The results show that the model can represent hemodynamic relationships in different ventricular and circulatory conditions and is able to react to the IABP assistance.

A hybrid mock circulatory system: development and testing of an electro-hydraulic impedance simulator

Mock circulatory systems are used to test mechanical assist devices and for training and research purposes; when compared to numerical models, however, they are not flexible enough and rather expensive. The concept of merging numerical and physical models, resulting in a hybrid one, is applied here to represent the input impedance of the systemic arterial tree, by a conventional windkessel model built out of an electro-hydraulic (E-H) impedance simulator added to a hydraulic section. This model is inserted into an open loop circuit, completed by another hybrid model representing the ventricular function. The E-H impedance simulator is essentially an electrically controlled flow source (a gear pump). Referring to the windkessel model, it is used to simulate the peripheral resistance and the hydraulic compliance, creating the desired input impedance. The data reported describe the characterisation of the E-H impedance simulator and demonstrate its behaviour when it is connected to a hybrid ventricular model. Experiments were performed under different hemodynamic conditions, including the presence of a left ventricular assist device (LVAD).

A hybrid (numerical-physical) model of the left ventricle

Hydraulic models of the circulation are used to test mechanical devices and for training and research purposes; when compared to numerical models, however, they are not flexible enough and rather expensive. The solution proposed here is to merge the characteristics and the flexibility of numerical models with the functions of physical models. The result is a hybrid model with numerical and physical sections connected by an electro-hydraulic interface - which is to some extent the main problem since the numerical model can be easily changed or modified. The concept of hybrid model is applied to the representation of ventricular function by a variable elastance numerical model. This prototype is an open loop circuit and the physical section is built out of a reservoir (atrium) and a modified windkessel (arterial tree). The corresponding equations are solved numerically using the variables (atrial and arterial pressures) coming from the physical circuit. Ventricular output flow is the computed variable and is sent to a servo amplifier connected to a DC motor-gear pump system. The gear pump, behaving roughly as a flow source, is the interface to the physical circuit. Results obtained under different hemodynamic conditions demonstrate the behaviour of the ventricular model on the pressure-volume plane and the time course of output flow and arterial pressure.