Investigation of Acoramidis-based ionic liquids as potential stabilizers of transthyretin using DFT calculations, molecular docking, and ADMET studies

Abstract

Transthyretin amyloidosis (ATTR) is a type of amyloidosis that characterize by abnormal deposition of the transthyretin protein in various organs. Acoramidis drug is considered a promising treatment for patients with ATTR. However, oral delivery of the insoluble Acoramidis is challenging due to its poor bioavailability and low solubility. In the present study, three Acoramidis-based ionic liquids (ILs) are reported to address this challenge. The biological activity and reactivity of these compounds evaluated using computational chemistry methods, including molecular DFT calculations, molecular docking and ADMET (Chemical absorption, distribution, metabolism, excretion, and toxicity) analysis. The solubility of the ILs is compared based on their polarity. The results showed that all ILs were more polar than the original Acoramidis. The highest dipole moment and solubility in water belonged to Acoradidis-CF₃COOH (IL1). Also, the calculated thermochemical data indicated that IL1 was more stable than the other two ionic liquids. Molecular docking studies showed that IL1 had the highest binding affinity (− 7.5 kcalmol⁻¹). In addition, it formed a greater number of critical contacts with transthyretin (TTR) residues. Also, ADMET studies suggested favorable predicted oral bioavailability for these compounds.

Introduction

Transthyretin amyloidosis (ATTR) is a rare, progressive form of amyloidosis characterized by the abnormal accumulation of the protein transthyretin (TTR) in organs, particularly the heart and nerves. The deposition of this protein in various organs and peripheral nerves causes dysfunction^1,2. The deposition of these amyloid fibrils in the heart can lead to cardiac dysfunction (cardiomyopathy, dysautonomia, heart failure with preserved ejection fraction, and peripheral polyneuropathy)^3,4. Although ATTR currently recognized as a rare disease, there is growing evidence suggesting that its prevalence is higher than previously thought⁵.

The mechanism of action of this disease is as follows: in the first stage, the TTR tetramer dissociates into its constituent monomers. In the next stage, misfolding of the resulting monomers and their aggregation leads to the formation of amyloid fibrils^6,7. Amyloid deposits can cause a wide range of clinical manifestations, depending on their type, location, and amount^8,9.

Some experts believe that this disease is not easily diagnosed because its symptoms are similar to those of other, more common diseases. This disease can develop in two different ways: hereditary and acquired¹⁰. Although this is a rare pathology, due to its severity and long-term damage, new treatments are continually developed and researched annually, using innovative technologies.

Recently, effective disease-modifying therapies such as TTR tetramer stabilizers and TTR gene silencing therapies have been developed for ATTR amyloidosis^11–15. Acoramidis is considered a promising treatment option for patients with ATTR, especially for those who do not respond to existing treatments or experience severe side effects. Its structure is optimized for high-affinity binding to the TTR protein, leading to effective stabilization^16,17.

This drug acts as a transthyretin (TTR) stabilizer, preventing its degradation into unstable monomers by binding to the transthyretin protein (TTR). This action prevents the misfolding of the TTR protein and inhibits the formation of amyloid fibrils that accumulate in ATTR disease and cause damage to body tissues¹⁸.

Although Acoramidis, similar to previously developed tafamidis, is used to stabilize TTR in its tetrameric form and prevents the formation of amyloidogenic monomers and the progression of amyloidosis, Acoramidis is more selective for TTR and is a stronger stabilizer compared to tafamidis¹⁹.

Acoramidis has been evaluated in a phase 3 clinical trial since 2023¹⁰. In clinical trials, Acoramidis represents a potential advancement in the treatment of ATTR amyloidosis, particularly for patients with cardiomyopathy or polyneuropathy¹⁰. Acoramidis launched by Bridge Biopharma in November 2024 and then approved by the FDA to reduce adverse cardiovascular outcomes in patients with cardiomyopathy due to TTR amyloidosis.

Ionic liquid (IL)-based oral delivery systems are potentially useful for enhancing the oral bioavailability of MTX and improving its pharmacokinetic (PK) and pharmacodynamic properties.

Today, one of the problems of the pharmaceutical industry is the low solubility and poor bioavailability of drugs. Various methods are reported to overcome these problems. These methods include prodrug services, solid dispersions, crystal engineering, nanosuspensions, salt formation, adsorption on high surface area carriers, and micelle systems. Among these methods, salt formation is used directly to improve solubility. In recent years, ionic liquids as a new research field in pharmaceutical sciences offer new prospects in this field. These materials, with their unique properties and diverse capabilities, can be significantly effective in the development of new drugs with higher efficacy and greater safety. The role of ionic liquids in the pharmaceutical industry includes increasing solubility and stability, controlled release, increasing permeability through biological membranes, and drug bioavailability. In recent years, these materials have played an effective role in the pharmaceutical industry and medical sciences.^20–23.

Sangeeta et al. reported the synthesis and in-silico study of 1,3-benzodioxole-based lidocaine-tagged ionic liquids with BSA²⁴. Sidiko et al. reported a spectroscopic and DFT study of imidazolium-based ionic liquids with the antibacterial drug levofloxacin²⁵. In 2024, a series of 1,3-benzodioxole-based procaine-tagged ionic liquids was investigated as anticancer drugs by Sangeeta et al. They investigated the molecular docking studies with tubulin protein²⁶. Kalhor et. al. designed anticancer ionic liquids based on natural products. They investigated the properties of this drug delivery system using combined MD/QM studies²⁷. Saraswat et al. have screened and prepared ionic liquid-AVDs conjugate to combat COVID-19 surge using DFT methods and molecular docking²⁸. In 2021, the investigation of the anticancer drug noscapine-based ionic liquids to enhance solubility using a DFT approach reported by Kumar et al.²⁹. In addition, our research group has recently studied cosparin-based ionic liquids as alkaloids against COVID-19 using a density functional theory approach based on B3LYP/6-31G* calculations and molecular docking³⁰.

In the present study, the design of three Acoramidis-based ionic liquids is reported, which addresses the challenge of oral drug delivery of the insoluble Acoramidis¹⁷. The solubility, biological activity and reactivity of these ILs then evaluated using molecular DFT calculations, molecular docking, and ADMET analysis.

Methods

DFT approach

In this study, we designed three ionic liquids based on Acoramidis. The calculations carried out with the Gaussian 09 suite of programs by using DFT and B3LYP functional³¹. The usual 6-31++G basis set employed in the calculations to achieve descriptors of reactivity and thermodynamic parameters of the ionic liquids. This basis set has been effective in hydrogen bonding studies, thus enabling us to obtain accurate and reliable results for our research^32,33. All calculations were performed using the SCRF method of the polarizable continuum model (PCM) in water solvent.

The dipole moment of a molecule plays a significant role in determining its solubility in water. Another important property of molecules is the first hyperpolarizability (β_tot) of the molecule. The first hyperpolarizability (β) indicates the displacement of electrons under the influence of an electric field. Factor β is studied using second harmonic generation (SHG). Molecules with very high β values have high solubility in water. β_tot refers to the total hyperpolarizability, defined as:

1

Another quantity of significance regarding a molecule is the vector component of first hyperpolarizability (β_vec) represented by:

2

If the B_vec of the molecule be located along the active groups involved in biological reactions, it leads to increased charge transfer or biological activity.

The Reduced Density Gradient (RDG) was obtained from Multiwfn 3.4.1 software³⁴, and rendered by the VMD 1.9.1 program³⁵. RDG is defined as³⁶:

3

where the ρ(r) is the electron density and ∇ρ(r) is the norm of the electron density vector.

Molecular docking

We used molecular docking to predict the interactions between ionic liquids and transthyretin amyloidosis at the atomic level. The docking analysis carried out using Auto Dock Vina, which enabled us to predict binding affinities of ligands³⁷. The X-ray crystal structure of protein (PDB ID: 4tlt) was retrieved from Protein Data Bank³⁸. Docking-compatible structural formats for the analyzed molecules and the Transthyretin amyloidosis were prepared using Viewer Lite. The first step in the molecular docking process involves identifying the enzyme’s active site, where the drug will interact. Therefore, first, by performing blind docking on the entire surface of the molecule, the active site of the enzyme identified. After identifying the active sites, focused docking performed by establishing a grid box at active site of TTR. The grid box that encloses amino acids domain involved in the binding active sites, had the dimension of 46.22 × 43.10 × 57.52 (x × y × z) with an exhaustiveness parameter of 8 and number of mode 9. Visualization and detailed analysis of interactions performed using the software packages Accelrys Discovery Studio and Chimera software.

Drug-likeness and pharmacokinetic properties

SwissADME³⁹ and ADMETlab⁴⁰ servers used to predict the pharmacokinetic and pharmacological properties. Aqueous solubility determined by the methods: ESOL, (ALI) logS, and (SILICOS-IT) logS. Lipophilicity predicted by iLOGP, WLOGP, MLOGP, SILICOS-IT, and XLOGP3 values.

Results and discussion

Physico-chemical properties

To investigate the solubility and stability properties of the proposed compounds, we considered several factors including dipole moment, hyperpolarizability, and thermodynamic parameters. Molecules with higher dipole moments are more soluble in water. The appropriate dipole moment also allows the molecule to better align itself in the active site of an enzyme or receptor. Increasing β_tot improves the non-covalent interactions of the molecule with proteins. Of course, the hyperpolarizability of a molecule may be high, but the more important factor is the orientation of the hyperpolarizability vector (B_vec). This factor is very important in the analysis of biologically active structures. The optimized structure of the studied derivatives is shown in Fig. 1.

Fig. 1.

optimized structure of IL1 (Acoradidis-CF₃COOH), IL2 (Acoradidis-Trimethyl phosphine), and IL3 (Acoradidis-Collin).

The values of dipole moment, β_tot, and B_vec of the designed ionic liquids are presented in Table 1.

Table 1.

Quantum chemical parameters of Acoramidis and designed ILs.

Compound	Dipole moment (debye)	Eg (eV)	Btot × 10−53 (C3m3J−2)	Bvec × 10−53 (C3m3J−2)
Acoramidis	4.33	4.09	508.98	397.68
IL1	11.34	5.02	2792.88	2751.48
IL2	3.37	3.36	1076.77	941.31
IL3	5.89	4.83	1643.61	1202.16

As can be seen from Table 1, the dipole moment of IL1 (11.34 Debye) is higher than both the parent drug and ionic liquids IL2 and IL3. Also, β_tot and B_vec of this ionic liquid are higher than IL2 and IL3. Therefore, IL1 predicted to perform better than IL2 and IL3 in terms of both water solubility and protein interaction.

The thermodynamic parameters of Gibbs free energy (ΔG), thermal enthalpy, and optimization energy (HF) of the designed ionic liquids are presented in Table 2.

Table 2.

The Optimization energy (HF), the thermal enthalpy (ΔH), and the Gibbs free energies (eV) of Acoramidis and designed ILs.

Compound	ΔH (kcalmol−1)	HF (kcalmol−1)	ΔG (kcalmol−1)
Acoramidis	− 637,856.66	− 638,060.71	− 637,904.40
IL1	− 968,419.60	− 968,652.12	− 968,480.63
IL2	− 927,129.28	− 927,410.66	− 927,190.36
IL3	− 819,108.58	− 819,415.61	− 819,170.23

As can be seen in Table 2, the thermal enthalpy of all designed ionic liquids was lower than that of Acoramidis. This results indicate that the all ILs are more stable than the parent drug and the highest stability (− 968,419.60 kcalmol⁻¹) belongs to IL1. The calculated Gibbs free energy of ILs also showed that all ionic liquids experienced a decrease in ΔG, and an increase in stability. Also, the optimization energy of IL1 (− 638,060.71 kcalmol⁻¹) showed that it was the most stable ionic liquids. Given that a more negative ΔG indicates a greater affinity of the drug for binding to the target, and greater biological activity. As a result, it is predicted that IL1 will have greater biological activity.

The theoretical IR spectra of Acoramidis and ionic liquids designed based on this drug are shown in Fig. 2. As can be seen in this figure, Acoramidis showed characteristic peaks at 3694, 3661, 1697, 1303, 1277, and 967 cm⁻¹ which are related to the N–H, OH, C = O, C-N and C-O stretching frequencies, respectively. Also, the characteristic peaks observed at 1375 and 592 cm⁻¹ belong to the N–H and OH bending mode, respectively. Comparison of the spectras showed that these regions is very similar in the spectra of Acoramidis and the designed ionic liquids. The only visible difference is related to the strong peaks at 1985 cm⁻¹ in IL1 and 1788 cm⁻¹in IL3. These frequencies belong to the stretching mode of the acidic OH, which has formed a hydrogen bond with the nitrogen atom. Usually, the intensity of these peaks strongly influence by the hydrogen bond and its strength.

Fig. 2.

IR spectra of IL1 (Acoradidis-CF₃COOH), IL2 (Acoradidis-Trimethyl phosphine), and IL3 (Acoradidis-Collin).

RDG scatter plots

RDG is a fundamental dimensionless quantity used to describe electron heterogeneity in density functional theory. RDG provides information about noncovalent interactions in molecular systems. Using RDG, the stability of complexes can be determined by hydrogen bonding, van der Waals forces, and even repulsive interactions. In RDG plots the blue-colored regions highlight strong attractive forces involving hydrogen bonding, green region corresponds to weak, non-covalent interactions, and Red Region indicates steric repulsion. The RDG plots of the acoramidis and the three ionic liquids discussed in this study is presented in Fig. 3.

Fig. 3.

The plot of reduced density gradient (RDG) scatter.

As shown in this figure, molecules exhibited a combination of the three most common types of interactions including strong hydrogen bonds for bonding, van der Waals interactions or π–π stacking for strengthening as well as the repulsive forces that can be a factor in establishing spatial equilibrium. This type of interactions is exactly what is expected from drug complexes.

Molecular docking

Here, molecular docking used to compare the binding strength of the designed ionic liquids with TTR to that of Acoramidis. Molecular docking studies investigate the behavior of the drug at the enzyme binding site. The results of molecular docking studies are a scoring function that indicates the ability of these compounds to bind to TTR and, consequently, the extent of their pharmacological effect. The interaction of the drug with the enzyme involves different types of bonds and interactions, including hydrophobic bonds, polar bonds, hydrogen bonds, and π–π interactions, which are crucial for the stability and properties of the ligand-enzyme complex. The docking results are presented in Table 3.

Table 3.

Docking properties of Acoramidis and designed ILs (Kcal mol⁻¹).

Compounds	B.E (Kcal mol−1)	Interactions
		Hydrogen bonds	Hydrophobic interactions
Acoramidis	− 6.7	SER76, SER91	ASP90,SER91, PHE78
IL1	− 7.5	SER76, PHE78, TYR105, ASP90	THR87,SER76, ASP90
IL2	− 6.8	GLU80, THR87, SER91	HIS79, GLU80, THR87 ASN89, ASP90, ARG94
IL3	− 6.9	SER76, TYR105, TYR96	ARG94, SER91

Acoramidis binds to the TTR protein, preventing its breakdown into unstable monomers. The more tightly the drug binds to the protein, the greater the stability of the protein, and as a result, the drug’s effects will increase. The docking results of Acoramidis and three Acoramidis-based ionic liquids showed that all four compounds were positioned correctly in the active channel of the TTR protein (Fig. 4).

Fig. 4.

The positions of Acoramidis and IL1 (Acoradidis-CF₃COOH), IL2 (Acoradidis-Trimethyl phosphine), and IL3 (Acoradidis-Collin) within the active site of TTR.

By examining the simulation results, it was determined that the key amino acids located near the protein binding site are PHE78, SER91, HIS79, ARG94, ASP90, ASN89, THR87, TYR105, GLU84, and SER76.

The docking results of the designed ILs and TTR proteins (Table 3) with negative binding energy values indicate a high and favorable affinity for binding of all four compounds to the TTR protein (Fig. 5). The strongest binding score (− 7.5 Kcalmol⁻¹) belongs to IL1.

Fig. 5.

ligand-TTR interactions of Acoradidis and IL1 (Acoradidis-CF₃COOH), IL2 (Acoradidis-Trimethyl phosphine), and IL3 (Acoradidis-Collin).

The docking results of Acoramidis indicated two strong hydrogen bonds with SER76, and two weaker bonds with SER91. Also, the formation of three van der Waals interactions with residues ASP90, SER91, and PHE78 led to a more stable acoramidis-TTR complex.

IL1 is bound to the protein by four hydrogen bonds with residues SER 76, PHE78, TYR105, and ASP90. The resulting complex is also stabilized by van der Waals interactions with THR87, SER76, and ASP90.

The protein complex with IL2 is formed through hydrogen bonding with GLU80, THR87, SER91, and is further stabilized by van der Waals interactions with HIS79, SER91, THR87, ASN89, ASP90, and ARG94.

IL3 is bound to the protein by four strong hydrogen bonds with residues SER76, TYR96, and TYR105. The resulting complex is also stabilized by van der Waals interactions with SER91 and ARG94.

Cheminformatics

To investigate biological activity and determine the appropriate distribution of a compound, it is essential to predict drug similarity and pharmacokinetic properties. Nowadays, in silico studies are one of the valuable methods for preliminary analysis of physicochemical and pharmacokinetic properties in the design of new drugs. These approaches will accelerate the process of designing new drugs, improving the properties of existing drugs, and designing more effective therapeutic agents. In silico docking results are summarized in Tables 4 and 5.

Table 4.

Physicochemical properties of Acoramidis and IL1 (Acoradidis-CF₃COOH), IL2 (Acoradidis-Trimethyl phosphine), and IL3 (Acoradidis-Collin).

Compound	Molecular weight (g mol−1)	Lipophilicity log(Po/pw)	Water solubility log(mol L−1)	QED	TPSA (A0)	NHA	NHD
Acoramidis	292.12	3.635	− 3.471	0.819	71.25	5	1
IL1	392.1	0.796	− 1.706	0.692	112.99	7	2
IL2	354.15	− 0.527	− 2.215	0.763	74.08	5	0
IL3	367.19	− 2.044	− 0.315	0.682	98.75	7	2

Table 5.

Absorption, distribution, and excretion properties of Acoramidis and IL1 (Acoradidis-CF₃COOH), IL2 (Acoradidis-Trimethyl phosphine), and IL3 (Acoradidis-Collin).

Compound	Caco 2 log (cms−1)	HIA (%)	HOB		PPB (%)	Cl (mL/min/kg)	T1/2 (h)
			F20%	F30%
Acoramidis	− 5.253	0.004	0.002	0.002	28.69	2.067	0.824
IL1	− 6.035	0.010	0.018	0.089	24.25	1.876	0.745
IL2	− 5.331	0.182	0.008	0.010	44.00	2.289	0.840
IL3	− 5.874	0.027	0.016	0.006	10.12	2.283	0.913

Furthermore, in silico ADMET studies have predicted that both Acoramidis and designed ionic liquids obey Lipinski’s rule of five. Analysis of LogS values shows that solubility has increased in all three ionic liquids compared to the parent drug. The maximum solubility in water is related to IL3.

The prediction of drug permeability and absorption are determined using the human colon adenocarcinoma cell lines (Caco-2), human intestinal absorption (HIA), and the human oral bioavailability (HOB). An oral drug must first pass through intestinal cell membranes to reach the systemic circulation. Caco-2, due to their morphological and functional similarities, are commonly used to estimate drug permeability in vivo. In addition, HOB is a key factor that determines the fate of a new drug in clinical trials. For any drug administered by the oral route, oral bioavailability is undoubtedly one of the most important pharmacokinetic parameters because it is the indicator of the efficiency of the drug delivery to the systemic circulation. Here, HOB is shown by two parameters F20% and F30% and determines the probability of oral absorption of drugs. Molecules with a bioavailability ≥ 20% classified as F20% − (Category 0), while molecules with a bioavailability < 20% classified as F20% + (Category 1). The output value is the probability of being F20% + , within the range of 0 to 1³⁷.

PPB is one of the main mechanisms of drug absorption and distribution, so the binding of a drug to plasma proteins has a significant influence on its pharmacodynamic behavior. PPB can directly affect oral bioavailability. A compound consider to have a good PPB, if the predicted PPB is less than 90%.

The drug excretion is determined using the clearance (CL) and the half-life (T_1/2). CL is concerned with the rate at which the active drug is removed from the body. Compound consider to have a high clearance, if the predicted CL is > 15 ml/min/kg. Empirical decision of a drug is excellent if T1/2 of drug = 0–0.3. The values of Caco-2, HIA, HOB, Cl, and T_1/2 of Acoradidis and their ILs are summarized in Table 5.

The data in Table 5 show that the intestinal permeability and absorption of Acoramidis were low. These values increased in all three ionic liquids. Also, the highest Caco 2 permeability and absorption are belonged to IL1 (− 6.035 log cms⁻¹) and IL2 (0.182%) respectively.

As can be seen from Table 5, the probability of oral absorption for Acoramidis was very low. This value has increased in the all ILs. Ionic liquid 1 has the highest probability of oral absorption (0.018%).

According to the data presented in Table 4, IL2 showed the highest distribution (44.00%). Also, the CL and T_1/2 values of Acoramidis predict poor elimination and half-life for this drug. The CL value for IL1 is improved compared to the parent drug.

Conclusion

Acoramidis is considered a promising treatment option for patients with ATTR, especially for those who do not respond to existing treatments or have severe side effects. However, oral delivery of the insoluble drug Acoramidis is challenging due to its poor bioavailability and low solubility. In the present study, three Acoramidis-based ionic liquids are reported to address this challenge. The biological activity and reactivity of these compounds are evaluated using computational chemistry methods, including molecular docking and density functional theory. Their pharmacokinetic properties are also investigated using the ADMET online site.

The calculated results of dipole moment, βtot, and Bvec showed that IL1 would have both higher solubility than the parent drug and the two ionic liquids 2 and 3, and would exhibit stronger interactions with the protein.

Also, the higher entropy and enthalpy of acoramidis-based ionic liquids compared to the parent drug indicate the greater stability of these compounds. The highest stability was belongs to IL1.

The docking results of Acoramidis and three designed ionic liquids showed that all four compounds are positioned correctly in the active channel of the TTR protein. Also, IL1 bounded to TTR protein with the most suitable binding energy. Consequently, IL1 was the most effective candidate in preventing the degradation of this protein.

Furthermore, in silico ADMET studies predicted that all four compounds obey Lipinski’s rule of five. Analysis of LogS values shows that solubility has increased in all three ionic liquids compared to the parent drug. The maximum solubility in water belongs to IL3.

Also, intestinal penetration and absorption values showed improvement of these values in designed ionic liquids compared to parent drug. The highest penetration and absorption values were related to ionic liquids 1 and 2, respectively. The probability of oral absorption of Acoramidis is very low. This value has increased in all three ionic liquids. Ionic liquid 1 has the highest probability of oral absorption.

According to the obtained data, IL2 has shown the highest distribution rate. CL values of Acoramidis predict slow excretion and a relatively short half-life for this drug. The CL for IL1 improved compared to the original drug. Comparisons among the three ionic liquids showed that IL1 balances solubility with stability and binding affinity.

Author contributions

Fatemeh Mostaghni: Writing—original draft, investigation, software, formal analysis, data curation. Writing—review and editing, resources, methodology. Nosrat Madadi Mahani: Writing—review and editing, supervision, resources, methodology.

Data availability

All data generated or investigated during this study are included in this published article.

Declarations

Competing interests

The authors declare no competing interests.