Table 2 shows the docking scores of all the designed compounds against the protein receptor, which were compared to the chloroquine standard. The number of hydrogen bonds, hydrogen bond energy, and interaction energy were all included in the table (Table 2). All the compounds (except D1, − 98.7673; D3, − 97.6691; D6, − 98.84; D13, − 101.897; and D15, − 96.0251 kcal/mol) were found to have a higher docking score than the chloroquine standard (− 102.393 kcal/mol). As a result, they have a higher binding affinity than the normal chloroquine. The higher interaction energies (Table 2) of compounds D2, D7, D9, D10, D11, D14, and D16 with energies of − 155.075, − 147.869, − 142.607, − 155.332, − 143.971, − 143.887, and − 141.429 kcal/mol, respectively, confirmed their better interaction with the target than the chloroquine standard (− 139.888 kcal/mol). As demonstrated in Table 3, the proposed ligands generated hydrogen bonds with active site residues such as LEU359, TYR356, PRO52, HIS56, ARG136, and TYR147. The hydrogen bonds for six of the most active ligands are detailed in Table 3. These compounds are D16, 5-((6-methoxy-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)amino)benzo[b]thiophen-4-ol; D2, N-(benzo[b]thiophen-5-yl)-6-ethyl-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine; D10, 5-((6-methoxy-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)amino)benzo[b]thiophen-6-ol; D11, N6, N6,5-trimethyl-N7-(4-methylbenzo[b]thiophen-5-yl)-[1,2,4]triazolo[1,5-a]pyrimidine-6,7-diamine; D7, N5-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)benzo[b]thiophene-4,5-diamine; and D9, 5-methyl-N7-(4-methylbenzo[b]thiophen-5-yl)-[1,2,4]triazolo[1,5-a]pyrimidine-6,7-diamine, with − 114.205, − 123.259, − 121.678, − 119.665, − 119.256, and − 116.174 kcal/mol re-rank scores, respectively. A hydrogen bond is formed between compound D16 and amino acid residue, LEU359 (H∙∙H∙∙O) with a bond distance of 2.2874 Å. The two hydrogen bonds formed between compound D2 and the active residues TYR356 (N∙∙H∙∙H) and PRO52 (H∙∙H∙∙O) have bond distances 2.12677 and 2.00418 Å, respectively, while those between D10 with the active residue HIS56 (O∙∙H∙∙H) and ARG136 (N∙∙H∙∙H) have bond distances 2.15191 and 2.27840 Å, respectively. The interactions of D11 with ARG136 (N∙∙H∙∙H) residue are at a 1.6277-Å bond distance. The three hydrogen bond interactions of D7 with TYR356 (N∙∙H∙∙H), TYR145 (H∙∙H∙∙O), and PRO52 (H∙∙H∙∙O) amino acid residues gave rise to 2.1607, 2.1484, and 2.3053 Å bond distances, respectively. The lone hydrogen bond formed between D9 and ARG136 (N∙∙H∙∙H) residue is at a distance of 1.6080 Å. The presence of hydrogen bonds, in addition to other hydrophobic interactions, may explain the high docking scores of the most active molecules. The binding modes as well as interaction images of the most active compounds, D16, D2, D10, D11, and D7, were exhibited in Fig. 2.
Drug-likeness and ADME prediction
The Lipinski, rule-of-five (Ro5), is used to assess the drug-likeness of chemical compounds and potential medicines. According to Lipinski’s Ro5, chemical compounds that can be utilized as pharmaceuticals should have a molecular weight (MW) of less than 500 g/mol, a logarithm of the partition coefficient (log P) of less than 5, hydrogen bond donors (HBDs) of less than 5, and a hydrogen bond acceptor (HBA) of less than 10 . Furthermore, the number of rotatable bonds (RotB) of ≤ 10 and a topological polar surface area (TPSA) of ≤ 140 Å2 [20, 22,23,24] have been observed to correlate with pharmacological flexibility and permeability, respectively. Compounds that meet these criteria have been shown to have better pharmacokinetics and bioavailability characteristics.
Low molecular weight (MW) signifies that the molecules are light and can easily pass through the cell membrane. Low molecular weight (MW 500) chemicals are favored for oral absorption , whereas compounds with MW > 500 Da are absorbed via an alternate route, generally the membrane . The research revealed that all of the data (Table 4) were less than 500 Da.
The implicit log P (IlogP) is the n-octanol/water partition coefficients of a particular molecule in two immiscible solvents; it dissolves the molecule in both solvents while maintaining the molecule’s neutrality. Initially, the IlogP was hired for biomedical and pharmaceutical research. IlogP plays a critical role in medication absorption in the mouth , as well as facilitating drug interactions with their biological targets . Because it possesses both hydrophilic and lipophilic qualities, n-octanol was thought to be a superb mimic of phospholipid membrane features . The estimated values of IlogP (Table 4) were found to be less than five (1.82–3.05), as recommended by Lipinski’s rule of five . As a result, the developed derivatives should have great oral absorption qualities.
H-bond acceptors (HBA) number is as follows: Any heteroatom with at least one bound hydrogen is referred to as a hydrogen bond acceptor. The sum of these heteroatoms (N and O atoms) should be fewer than 10 according to the Lipinski rule of five . The H-bond acceptors determined for the intended compounds (Table 4) ranged from 3 to 5, which is significantly less than the Ro5 projected maximum limit.
H-bond donor (HBD) count is as follows: Any heteroatom lacking a formal positive charge, save pyrrole nitrogen, halogens, sulfur, heteroaromatic oxygen, and higher oxidation states of nitrogen, phosphorus, and sulfur, but including the oxygens connected to them, is referred to as a hydrogen bond donor. The amount of hydrogen bond donors (the sum of the OH and NH groups) should be less than or equal to 5 according to the Ro5. As can be seen in Table 4, all of the HBD values obtained were less than 5. Both HBA and HBD were critical because they synergize between chemicals and macromolecules, as well as having the potential to determine oral absorption .
The TPSA of a molecule is the sum of all polar atoms (oxygen, nitrogen, and their connected hydrogens) on the molecule’s surface, calculated by adding all polar fragments . The goal of the TPSA is to predict drug transport qualities such as intestinal absorption  and BBB penetration . For virtual screening and ADME property prediction, TPSA has gained prominence in medicinal chemistry . When the quantitative value of TPSA is < 140 Å2, it becomes a good predictor of intestinal absorption, and when it is < 60 Å2, it indicates good blood-brain barrier penetration . The proposed derivatives’ TPSA values (Table 4) were found to range from 83.35 to 118.60 Å2. This indicates that the results are less than 140 Å2, indicating that intestinal absorption is good. However, because the TPSA values are larger than 60 Å2, the proposed derivatives do not penetrate the blood-brain barrier well, as evidenced by the BBB determination (Table 5).
The total number of rotatable bonds (RBN) is equal to the total number of bonds that may freely spin around themselves. They are non-ring single bonds with a nonterminal heavy atom attached (i.e., non-hydrogen). Molecules with less than ten rotatable bonds have been reported to have better oral availability . The number of rotatable bonds for the developed compounds was determined to be less than 5, indicating that the developed compounds had a good oral bioavailability.
The in silico ADME studies involve investigating some pharmacokinetic properties of the designed compounds such as molar refractivity (MR), log of skin permeability (log Kp), blood-brain barrier (BBB) penetration, permeability glycoprotein (Pgp) substrate, gastrointestinal (GI) absorption, and cytochrome P450 (CYP450) enzymes: CYP1A2, CYP2C9, and CYP2C19 inhibitors. The reciprocal of the volume of a mole of a substance is defined as the molar refractivity (MR). The overall polarizability of a mole of a substance is related to molar refractivity. Molar refractivity data provide information about the electronic polarizability of individual ions in solution . The refractive index results can be used to explain molecular interactions in solution . The molar refractivity value should be between 40 and 130 for good absorption and oral bioavailability. Acceptable molar refractivity values, in combination with the number of rotatable bonds, indicate that substances have adequate intestinal absorption and oral bioavailability . The designed compound's MR values range from 82.7 to 99.85 m3/mol. This indicates that the proposed compounds have good intestinal absorption and oral bioavailability.
Permeability is a critical component of drug research since it predicts metabolite absorption, distribution, metabolism, and excretion (ADME). The ability of molecules to penetrate the outer layer of the skin is described by skin permeability (Kp) . The Kp includes assessing a compound's biological absorption via the skin and has been used as a source of data for threat assessment on the skin . The developed compounds’ log Kp values (Table 5) were all determined to be within the permissible range of − 8.0 to − 1.0 .
The blood-brain barrier is a microvascular endothelial layer of cells that surrounds the central nervous system (CNS) (BBB). The BBB is a structural and chemical barrier that prevents various medications from entering the brain, making the use of newly produced medications in the treatment of brain illnesses or other brain-related issues ineffective. Several prospective therapeutic compounds have been discovered to provide a significant obstacle to therapeutic research for central nervous system illnesses if they have minimal or no BBB penetration. The results of the BBB permeability test performed on our proposed derivatives (Table 5) demonstrated that all of them lack BBB permeability, making their application in the treatment of cerebral malaria futile.
The adenosine triphosphate (ATP)-binding cassette-transporter permeability glycoprotein (Pgp) functions primarily as a carrier-mediated primary active efflux transporter. P-glycoprotein can bind to a wide variety of substrates, which are widely distributed throughout the body. Pgp transporters are located in the small intestine, blood-brain barrier capillaries, and several critical organs such as the kidney and liver . Substances can enter the cell via active transport or passive diffusion, and they can be effluxed with the help of Pgp. The Pgp affects the absorption, distribution, and clearance of a variety of substances. As a result, identifying permeability glycoprotein substrates is critical for identifying prospective medicines and optimizing them. Pgp substrate was detected only in the proposed compounds D7, D9, D13, and D14.
Cytochrome P450 (CYP) enzymes are a family of proteins involved in the synthesis and metabolism of a wide range of internal and exterior cellular components. These enzymes have been found in animals, plants, microorganisms, and even a few viruses. They get their name from the fact that they are linked to the cell membrane (cyto) and contain heme pigment (chrome and P), which produces a 450 nm spectrum when combined with carbon monoxide.
In humans, heme-containing cytochromes P450 (CYPs) are a superfamily of enzymes that break down a variety of endogenous and xenobiotic substances. More than 50 isoforms of CYP enzymes exist, with 1A2, 2C9, 2C19, 2D6, and 3A4 isoforms accounting for over 90% of oxidative metabolic processes . Inhibitory drug metabolism fails when CYP enzymes are inhibited. During medication development, studying the inhibitory activity of proposed derivatives against a certain CYP isoform becomes a critical factor. Table 5 shows the results of the inhibitory prediction for three CYP isoforms (CYP1A2, CYP2C9, and CYP2C19). While all of the proposed compounds were anticipated to inhibit CYP1A2, just a few derivatives (D7, D10, and D13–16) were found not to inhibit CYP2C19, and just three derivatives (D5–7) were found to inhibit CYP2C9.