Novel Thiourea and Oxime Ether Isosteviol-Based Anticoagulants: MD Simulation and ADMET Prediction.

Activated blood coagulation factor X (FXa) plays a critical initiation step of the blood-coagulation pathway and is considered a desirable target for anticoagulant drug development. It is reversibly inhibited by nonvitamin K antagonist oral anticoagulants (NOACs) such as apixaban, betrixaban, edoxaban, and rivaroxaban. Thrombosis is extremely common and is one of the leading causes of death in developed countries. In previous studies, novel thiourea and oxime ether isosteviol derivatives as FXa inhibitors were designed through a combination of QSAR studies and molecular docking. In the present contribution, molecular dynamics (MD) simulations were performed for 100 ns to assess binding structures previously predicted by docking and furnish additional information. Moreover, three thiourea- and six oxime ether-designed isosteviol analogs were then examined for their drug-like and ADMET properties. MD simulations demonstrated that four out of the nine investigated isosteviol derivatives, i.e., one thiourea and three oxime ether ISV analogs, form stable complexes with FXa. These derivatives interact with FXa in a manner similar to Food and Drug Administration (FDA)-approved drugs like edoxaban and betrixaban, indicating their potential to inhibit factor Xa activity. One of these derivatives, E24, displays favorable pharmacokinetic properties, positioning it as the most promising drug candidate. This, along with the other three derivatives, can undergo further chemical synthesis and bioassessment.

Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.

The Nep1 protein is essential for the formation of eukaryotic and archaeal small ribosomal subunits, and it catalyzes the site-directed SAM-dependent methylation of pseudouridine (Ψ) during pre-rRNA processing. It possesses a non-trivial topology, namely, a 31 knot in the active site. Here, we address the issue of seemingly unfeasible deprotonation of Ψ in Nep1 active site by a distant aspartate residue (D101 in S. cerevisiae), using a combination of bioinformatics, computational, and experimental methods. We identified a conserved hydroxyl-containing amino acid (S233 in S. cerevisiae, T198 in A. fulgidus) that may act as a proton-transfer mediator. Molecular dynamics simulations, based on the crystal structure of S. cerevisiae, and on a complex generated by molecular docking in A. fulgidus, confirmed that this amino acid can shuttle protons, however, a water molecule in the active site may also serve this role. Quantum-chemical calculations based on density functional theory and the cluster approach showed that the water-mediated pathway is the most favorable for catalysis. Experimental kinetic and mutational studies reinforce the requirement for the aspartate D101, but not S233. These findings provide insight into the catalytic mechanisms underlying proton transfer over extended distances and comprehensively elucidate the mode of action of Nep1.

The Reaction Mechanism of Loganic Acid Methyltransferase: A Molecular Dynamics Simulation and Quantum Mechanics Study.

In this work, the catalytic mechanism of loganic acid methyltransferase was characterized at the molecular level. This enzyme is responsible for the biosynthesis of loganin, which is a precursor for a wide range of biologically active compounds. Due to the lack of detailed knowledge about this process, the aim of this study was the analysis of the structure and activity of loganic acid methyltransferase. Using molecular dynamics (MD) simulations, the native structure of the complex was reconstructed, and the key interactions between the substrate and loganic acid methyltransferase were investigated. Subsequently, the structures obtained from the simulations were used for quantum chemical (QM) calculations. The QM calculations allowed for the exploration of the energetic aspects of the reaction and the characterization of its mechanism. The results obtained in this study suggest the existence of two patterns of interactions between loganic acid methyltransferase and the substrate. The role of residue Q38 in the binding and orientation of the substrate's carboxyl group was also demonstrated. By employing a combined MD and QM approach, the experimental reaction barrier was reproduced, and detailed insights into the enzymatic activity mechanism of loganic acid methyltransferase were revealed.

The Connectivity Matrix: A Toolbox for Monitoring Bonded Atoms and Bonds.

The concept of a connectivity matrix, essential for the reaction fragility (RF) spectra technique for monitoring electron density evolution in a chemical reaction, has been supported with a novel formulation for the diagonal matrix elements; their direct link to the electron density function ρ(r) has been demonstrated. By combining the concept with the atomization energy of a system, the separation of the potential energy into atomic and/or bond contributions has been achieved. The energy derivative diagrams for atoms and bonds that are variable along a reaction path provide new insight into the reaction mechanism. Diagonalization of the connectivity matrix resulted in the eigenvectors that provide information on a role of individual atoms in the development of structural changes along a reaction path.

Bond Softening Indices Studied by the Fragility Spectra for Proton Migration in Formamide and Related Structures.

Computational scheme to obtain bond softening index λ, defined within the conceptual DFT, has been obtained with the use of the reaction fragility (RF) concept. Numerical results were obtained with the RF spectra for the proton transfer reaction in formamide molecule (H2NCHO) and the water assisted proton migration in H2NCHO·H2O complex. Double proton transfer reaction in the formamide dimer, (H2NCHO)2, and its analogues, (H2NCHS)2 and (H2NCHO)·(H2NCHS), have also been studied. The atomic and bond RF spectra clearly describe the density reorganization in the backbone of each molecule, resulting from proton displacement in the systems. The obtained softening indices have been calculated for hydrogen atoms in the reactant state (RS) and product state (PS) configuration. These indices provide fine characteristics for the local sensitivity of the reacting system to a disturbance of the position of a chosen atom.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

The reaction fragility spectrum.

We report an original method that provides a new insight into the reaction mechanism by direct observation of bond breaking and formation. Variations of the diagonal elements of the Hessian along the IRC are shown to reflect the anharmonic properties of the system that are induced by electron density modifications upon the reaction. This information is presented in the form of the reaction spectrum, demonstrating how particular atoms engage in the reorganization of bonds. The test reactions are: HCOF synthesis and HONS isomerization.

Atomic Resolution for the Energy Derivatives on the Reaction Path.

Definite algorithms for calculation of the atomic contributions to the reaction force Fξ and the reaction force constant kξ (the first and the second derivatives of the energy over the reaction path step) are presented. The electronic part in the atomic and group contributions has been separated, and this opened the way to identification of the reactive molecule fragments on the consecutive stages of the reaction path. Properties have been studied for the two canonical test reactions: CO + HF → HCOF and HONS → ONSH.

Variation of the electronic dipole polarizability on the reaction path.

The reaction force and the electronic flux, first proposed by Toro-Labbé et al. (J Phys Chem A 103:4398, 1999) have been expressed by the existing conceptual DFT apparatus. The critical points (extremes) of the chemical potential, global hardness and softness have been identified by means of the existing and computable energy derivatives: the Hellman-Feynman force, nuclear reactivity and nuclear stiffness. Specific role of atoms at the reaction center has been unveiled by indicating an alternative method of calculation of the reaction force and the reaction electronic flux. The electron dipole polarizability on the IRC has been analyzed for the model reaction HF + CO→HCOF. The electron polarizability determined on the IRC α e (ξ) was found to be reasonably parallel to the global softness curve S(ξ). The softest state on the IRC (not TS) coincides with zero electronic flux.