De novo nonalcoholic steatohepatitis inhibiting drug design

Abstract

A newly developed molecule has been created through computer-aided drug design techniques to efficiently suppress and control the α-helical topology of β2-Spectrin., effectively preventing Non-alcoholic Steatohepatitis (NASH) disease.

Description

[0001] DE NOVO NONALCOHOLIC STEATOHEPATITIS INHIBITING DRUG DESIGN

[0002] Technical Field of the Invention

[0003] The present invention relates to a new molecule which can suppress Non-alcoholic Steatohepatitis (NASH) via modulating the P2-Spectrin to halt the spread of the disease.

[0004] State of the Art of the Invention (Prior Art)

[0005] To eliminate Non-alcoholic Steatohepatitis (NASH) once and for all, one should study the silencing of the gene of SPTBN1 or the suppression of the expression of P2-Spectrin or the inhibition of P2-Spectrin since it overexpresses.

[0006] The first approach is the regioselective drug design that will target any specific recurring nucleotides base within the 220,000 nucleotides of SPTBN1 in Chromosome 2 which is quite difficult since its modelling and simulation studies would require thousands and thousands of GPUs in supercomputers and would require months if not years.

[0007] However, as a second approach solving the issue, designing a siRNA that would serve as a drug to suppress the expression of P2-Spectrin might yield a valuable solution. However, this might be a risky one in terms of counter-indications of the drug since Spectrin proteins are quite essential in terms of structural stability of the phospholipids of the cell membrane and the cell morphology could be lost if too many spectrins are eliminated from the media before they could be expressed.

[0008] The third approach could be the case of NASH where P2-Spectrin accumulates too much due to inflammation and it must be inhibited but not eliminated entirely as was mentioned in the second approach. Due to this reason, de novo drug design can be done to both inhibit and modulate the activity of P2-Spectrin to prevail over the NASH symptoms and its inflammatory problems to its own tissue. Brief Description and Objects of the Invention

[0009] In the present invention, a novel drug molecule has been synthetically designed using computer-based methods to selectively target P2-Spectrins and effectively decrease and suppress the proliferation of NASH disease. Computational software tools, including molecular docking and molecular dynamics (MD) were utilized to demonstrate the drug's high efficiency in suppressing and regulating the a-helical topology of P2-Spectrin. This protein plays a critical role in the disease pathway.

[0010] All in all, it has been achieved a successful design for this molecule with its pharmaceutical organic chemistry possessing sulphur groups for further affinity towards the receptor was chosen as can be seen in Figure 1 where its inhibition factor is higher than any molecule within the scientific literature depending on the results in Figure 4. Thus, by backing this molecule’s chemistry with strongly proven computational software, this is quite a valuable bioorganic structure that should be patented where its innovative design has the potential to demonstrate promising results in in vitro, in vivo, ex vivo, and human phase stages.

[0011] The newly designed drug molecule provides very good inhibition of binding energy A(AG) above -10 / -11 kcal / mol so that the strong binding and inhibition of the active sites of protein P2-Spectrin can be proven. The designed drug has remarkable ability to efficiently suppress and control the a-helical topology of P2-Spectrin.

[0012] Definitions of Figures Describing the Invention

[0013] The figures and related descriptions used to better explain the molecule designed by this invention are as follows.

[0014] Figure 1: The chemical structure of de novo designed drug.

[0015] Figure 2: De novo designed molecule (on the left) docks on the isolated P2- Spectrin (on the right) under the pH of 7.3 to suppress NASH disease.

[0016] Figure 3: Designed molecule-P2-Spectrin complex with the inhibition A(AG) binding energy of -13.9 kcal / mol.

[0017] Figure 4: The cluster analysis of all the docked poses. Detailed Description of the Invention

[0018] This present invention, in silico study that was performed, provides more insights into the non-bonding intermolecular interactions between drug-protein to decipher the inhibition efficiency to explore the role of H-bonding in the drug binding mechanism.

[0019] The goal here is to initiate the research with computational tools to illustrate efficiently how the drug matches the domains of P2- Spectrin (Figure 1 and 2) and therefore determine the protein binding affinity, inhibition, binding mechanism, and efficiency of the drug.

[0020] To achieve such a goal, it should be known that the effectiveness of interactions appears to depend on various factors, including the affinity of the drug's external groups to the protein, and the topology of the binding.

[0021] The main idea is to simulate and compute the theoretical stability of P2-Spectrin under the inflammatory conditions of a liver cell’s pH of 7.3 and compare its AG when it forms a complex of designed molecule-P2-Spectrin.

[0022] Theoretical Geometric Optimization

[0023] To accurately determine the active sites of a molecule and investigate its interactions with receptors, it is essential to establish its optimal geometric structure. In this study, de novo designed molecule has been utilized as the ligand's organic chemical structure and analyzed its most stable molecular geometry using the Gaussian 09 program with density functional theory (DFT) / B3LYP functional and the 6-31G(d,p) basis set. This process has been resulted in the formation of the most stable molecular structures of de novo molecule with P2-Spectrin, intended for further computational and simulation-based research, as depicted in Figure 2 and Figure 3. To prepare input files for molecular docking, molecular dynamics computations, and post-processing of output files, GaussView 6.0 and Avogadro 1.95 software programs have been employed.

[0024] Molecular Docking Procedure

[0025] Molecular docking simulations have been conducted using the AutoDock Vina 1.1.2 software program, renowned for its exceptional precision and accuracy in biochemical docking simulations. A total of 800 poses have been generated, comprising 100 poses for each simulation. Blind docking has been employed, and the grid box dimensions have been set to 80 x 80 x 100 A3. The ligand which is de novo designed molecule has been studied in its interactions with the receptor structure of P2-Spectrin, downloaded with the PDB id of 6M3P and isolated from the protein complex for analysis. Gauss View 6.0 and Avogadro 1.95 software programs have been utilized for the optimization of the ligands and 1BNA structures. The simulations have been effectively illustrated the interactions and binding of the drug to the receptor, with the docking scores represented in kcal / mol signifying the Gibbs free binding energy. From all the simulations, the initial structure and input file for the subsequent molecular dynamics (MD) simulations have been selected as the docking pose with the most accurate and favourable binding energy, identified within the best-clustered data.

[0026] Molecular Dynamics (MD) Simulations

[0027] The initial structures for the MD simulations have been chosen based on the docking poses with the most favourable binding energies, as previously reported in scientific literature. The molecular dynamics (MD) simulations have been conducted using Schrodinger’s Maestro Desmond Program, each spanning 50 ns with 5000 poses at 10 ps intervals. To ensure accuracy, each MD simulation was repeated five times with different seed numbers, confirming the correctness of the simulation parameters and the structures of the de novo designed molecule-P2 Spectrin complexes have been formed.

[0028] During the MD simulations, the dynamic properties of the ligand-receptor complexes have been continuously evaluated over time. The simulation area has been defined by a grid box measuring 130 x 130 x 130 A3with a spacing of 0.5A, providing extensive grid area for the simulations. TIP3P-type water molecules have been included within the box, and 0.15 M NaCl ions have been added to neutralize the system. The temperature and pressure conditions have been set as follows: NPT at 310 K with Nose-Hoover temperature coupling and a constant pressure of 1.01 bar using Martyna Tobias-Klein pressure coupling. The system has been unconstrained, and the default fitting for OPLS 3.0 standards have been provided the initial velocity values for the forcefield calculations.

[0029] Furthermore, the formation of hydrogen bonds during the interaction of ligands with P2 Spectrin have been investigated during the MD simulations. Figure 3 illustrates the main pose of the de novo designed molecule-P2-Spectrin complex, taken under 3D video within Schrodinger’s Maestro Desmond MD software, where each MD run has 5000 frames. Designed molecule is strongly attached to the groove active site of P2- Spectrin. Along with the MD results in Schrodinger’s Maestro Desmond and according to the cluster analyses of 100 posed trials from the molecular docking studies in Autodock Vina, it forms strong H-bonds P2-Spectrin with and the obtained docking energies are around -14 kcal / mol. The potential drug which is de novo designed molecule in scope of the invention bends the morphological alpha-helical structures of P2-Spectrin. De novo designed molecule inhibits and bends the alpha-helical structure morphology of P2-Spectrin via very strong H- bonds.

[0030] Table 1. The Computed Bioactivity Scores and Physical Properties of Designed Molecule

[0031] As can be seen from Table 1, from the computed bioactivity data, the molecule of interest seems very bioactive towards the most significant proteins. This data vindicates a further check for the chemical structure correctness and versatility of the designed drug molecule. Depending on the cluster analyses in Figure 4, there were two main clusters which is a good result indicator and expected to happen for strong binding, inhibiting drugs as in the scientific literature. The two main clusters have similar binding energies that are around -14 kcal / mol.

[0032] With such high docking score, a-helical modulation, and a bioactive molecule along with great cluster results that can pass the in vitro and clinical tests depending on the data at hand, the molecule formula should be patented before going into further pre-clinical and clinical studies.

Claims

CLAIMS1. A computational designed molecule capable of suppressing and controlling the a- helical topology of P2-Spectrin, the molecule having the formula:

2. Use of the computational designed molecule according to Claim 1 as an inhibitor of the P2- Spectrin receptor.

3. Use of the computational designed molecule according to Claim 1 as a suppressor of the P2- Spectrin receptor.

4. Use of the computational designed molecule according to Claim 1 as a modulator of the P2- Spectrin receptor.

5. Use of the computational designed molecule according to Claim 1 as a medicament.

6. A computational designed molecule according to Claim 1 for use in the treatment of Non-alcoholic Steatohepatitis (NASH) disease.

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