IN-SILICO ASSESSMENT VIA MOLECULAR DOCKING AND ADMET PROFILE OF BOTANICAL DRUGS (BERGAMOTTIN AND CASTICIN) AGAINST TRIAL DRUGS FOR LASSA VIRUS

IN-SILICO ASSESSMENT VIA MOLECULAR DOCKING AND ADMET PROFILE OF BOTANICAL DRUGS (BERGAMOTTIN AND CASTICIN) AGAINST TRIAL DRUGS FOR LASSA VIRUS

Ibrahim Asiata Omotayo, Adepoju Adewusi John, Olafare Oluwafemi Gbenga, Abdul-Hammed Misbaudeen, Latona Dayo Felix, Oyebamiji Abel Kolawole and Semire Banjo *

Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Oyo-State, Nigeria.

ABSTRACT: Lassa fever is a serious viral haemorrhagic illness caused by Lassa virus, a family of Arenaviridae. This haemorrhagic fever has become rampant in West Africa especially in Sierra Leone, the Republic of Guinea, Liberia and Nigeria, through exposure to food or household items contaminated with urine or faeces of infected Mastomys rats. There has been no vaccines or particular antiviral agents/drugs against the treatment of Lassa fever, but some drugs such ribavirin, lacidipine, phenothrin and remdesvir are being used in the early stage of the illness. The goal of the present work was to use in-silico methods via molecular docking and ADMET properties to assess the effectiveness of these drugs alongside the botanical drugs (Bergamottin and Casticin) found in grapefruits and Artemisia annua. The results showed that Remdesvir possesses outstanding inhibitory action against nucleoprotein (NP) of the Lassa virus, although Phenothrin and Casticin were active against 3MWP, Lacidipine and Casticin were active against 3MWT, 3MX5 and 3T5Q and Bergamottin, and Casticin were against 3T5N and 4FVU; Thus Remdesvir and Casticin (a botanical drug) could be used satisfactorily for the treatment of  lassa fever.

Keywords: Lassa fever, Botanical drugs, Remdesvir, Molecular docking, ADMET

INTRODUCTION: Mastomys natalensis, a peridomestic multimammate rodent, is a natural reservoir of Lassa fever virus. Mastomys rodents are well distributed throughout the sub-Saharan West Africa ¹.  It has been reported that Hylomyscus pamfi and Mastomys erthrocyclus species are major reservoirs, as well as carriers of lassa virus.

This virus from Mastomys finds its way into humans through direct contact with rodent excreta, rodent bites, rodent urine, as well as through handling and eating of rodents; these are common in rural areas in West African countries ^{2, 3}. Lassa virus belongs to a family of Arenaviridae, a genus Mammarena virus.

The hemorrhagic fever has become rampant in West Africa especially in Sierra Leone, the Republic of Guinea, Liberia and Nigeria ^{4, 5}, this fever gets to its peak in the dry seasons. The Nigeria Centre reported for Disease Control that in 2020, over 4,761 suspected cases were reported, with about 15-20% of the cases developed into active hemorrhagic fever by 17^th May, 2020 ⁶. The overall rate of fatality has been estimated to be 1%; however, the mortality rate can be as high as 50% during epidemics ⁷. The period of incubation of Lassa fever is between six to twenty-one days after infection, and its symptoms similar to that of typhoid fever and malaria. The early symptoms include weakness, sore throat, body pains, malaise, fever, nausea, diarrhea, vomiting, and cough ^{8, 9}, while the later stage symptoms include mucosal and internal bleeding, seizures, disorientation, coma and deafness ⁸. Till date, there is no vaccines or particular antiviral agents/drugs against the treatment of Lassa fever; however, therapeutic approaches are limited to the administration of ribavirin in the early stage of the illness. Others drugs such as Lacidipine, Phenothrine and Remdesvir have been identified as entry inhibitors of lassa virus by blocking low-pH-induced membrane fusion ¹⁰.

More recently, the use of medicinal plants extracts for the treatment of virus-related diseases are now being recognized as a result of prevalence in drug-resistant virus diseases; therefore, more of plant extracts are now being tested against the resistant strain. Bergamottin and Casticin are two compounds found in grapefruits and Artemisia annua respectively; these compounds have been found to be active against lassa virus.  Bergamottin, known as 5-geranoxypsoralen, is a natural furanocoumarin found in the pomelos pulp, peel and pulp of the bergamot orange ¹¹, whereas, Casticin is a methyoxylated flavonol, also found in Vitex agnus ^12,13.

Casticin has inhibited LASV entry by blocking low-pH-induced membrane fusion, F446L mutation, located in the transmembrane domain of GP2 is resistance to casticin ^14-16. However, bergamottin has shown to slightly affect LASV GPC-mediated membrane fusion, inhibiting LASV entry by blocking endocytic trafficking ^{14, 17-19}. Remarkably, both bergamottin and casticin have been reported to show inhibitory effects on authentic lymphocytic choriomeningitis virus ¹⁴. However, in this present work, in-silico methods were used to assess the potency and safety of Bergamottin and Casticin; the two botanical drugs via molecular docking and ADMET profiling. The results were compared with four commercial drugs (Lacidipine, Phenothrine, Remdesvir and Ribavirin) that are being used for the treatment of patients with Lassa fever, these drugs are were docked against nucleoprotein (NP) of the Lassa virus; 3MWP, 3MWT, 3MX2, 3MX5, 3T5Q, 3T5N, 4FVU and 4GV9 ^20-24. The NP for the RNA synthesis and immune suppression (3MWP, 3MWT, 3MX2, 3MX5) ²⁰, the arenavirus NP for the genomic ribonucloe protein complexes, (3T5Q and 3T5N) ²¹ which are critical for transcription and replication of the viral genome, involving in RNA-binding domain of Lassa virus NP in complex with ssRNa. 4FVU ²² involves indigestion of NP exonuclease activity, which causes suppression of innate immune signaling in the infected cell, and 4GV9,3’-5’ exoribonuclease ²³ suppresses type 1 interferon (IFN) production by degrading the immune stimulatory RNAs.

The protein receptors were downloaded from the Protein Data Bank (PDB), a depository data bank that contains 3D structural information of large biological molecules such as proteins and nucleic acids (https://www.rcsb.org/structure). Also, the SDS format of the ligands was gotten from the PubChem database (https://pubchem.ncbi.nlm.nih.gov) and then taken to cactus online smiles translator (https://cactus.nci.nih.gov) for ligand download.

IN-SILICO METHODS:

Molecular Docking Procedures: The equilibrium conformers were searched for downloaded ligands with Austin Model 1 (AM1) of the semi-empirical AM1 method. The lowest energy conformer of each ligand was used as starting structure for optimization with Density Functional Theory (DFT) method of Becke’s three-parameter hybrid functional with correlation of Lee, Yang and Parr (B3LYP) ^{24, 25} with 6-31G** basis set. The minima equilibrium optimization was verified by frequency calculations characterized by positive harmonic frequencies ^{26, 27} as implemented in Spartan 14 ²⁸. These optimized structures of the ligands were now used for molecular Dockingsimulations. Docking of the proteins with the ligands or inhibitors was carried out using Discovery studio, Autodock Tool 1.5.6. On the Autodock tool, AutoDock Vina 1.1.2 and Edupymol version 1.7.4.4.  Discovery studio was used to clean up and repair the receptor, while Edupymol was used as a visualizer. Autodock Tool was used to set the grid box around the binding site of the proteins as observed in the crystal structures, polar hydrogen atoms were first added to the proteins followed by Gasteiger charges calculation before setting the grid box. The protein files were saved as pdbqt file prior to docking simulation with AutoDock Vinato to calculate binding affinity and Interactions between the ligand and proteins were visualized using discovery studio 2019 ^29-39. However, 3DLigandSite -Ligand binding site prediction Server (https://www.wass-michaelislab.org/3dlig/) was used to identify the active gorge of the proteins based on ligand-binding sites predictions using similar structures ⁴⁰.

Pharmacokinetics Profile: The smiles structures of drugs/ ligands downloaded from the PubChem database were used for the physicochemical and ADMET profiles of the ligands to assess the qualitative pharmacokinetics properties viz; absorption, distribution, metabolism, excretion, and toxicity by using ADMET Predictor 9.5 installation (www.simulations-plus.com).

RESULTS AND DISCUSSION:

Docking Conformation and Binding Affinity:

Docking with 3 MWP: Several conformations were achieved from the docking simulation of the studied compounds. The superlative conformation (conformation with lowest binding free energy) is presumed to be the conformation with binding energy in relation to the inhibitory constant (Ki).

The predicted binding energies for all the studied drugs (Bergamottin, Casticin, Lacidipine, Phenothrin, Remdesvir and Ribavirin) with 3 MWP receptor showed that Remdesvir has the binding affinity of -9.1 kcal/mol; Phenothrin -8.6 kcal/mol, Casticin -8.3 kcal/mol, Bergamottin -7.2 kcal/mol, Ribavirin -6.5 kcal/mol and Lacidipine -6.3 kcal/mol.

The inhibitory constant (Ki) of the drugs ranges from 0.21 – 23.96µM; Remdesvir 0.21 µM, Phenothrin 0.49 µM, Casticin 0.82 µM, Bergamottin 5.24 µM, Ribavirin 17.10 µM and Lacidipine 23.96 µM; the higher the binding affinity, the lower the inhibition constant and vice versa ⁴¹ as shown in Table 1. The H-bond distances between amino acid residues in the binding purse and drug range from 1.8 to 3.5Å, and other forms of interactions between the ligand and the receptor are displayed in Fig. 1.

TABLE 1: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 3MWP RECEPTOR WITH THE LIGANDS

Bergamottin showed hydrogen bond with GLY'249 and TYR'209; Casticin formed H bond with SER'9, TYR'209 and GLU'266; Lacidipine with TRP'331, GLU'107 and GLN'442; Phenothrin with ARG'300; Remdesvir with LYS'167, LEU'550, VAL'549, ARG'556, GLU'170, ALA'169, ARG'118, ARG'118 and ASN'168; Ribavirin with SER'238, GLU'117, ARG'300, ARG'300 and ASN'174.

The order of binding affinity in relation to the drug activeness against 3MWP are Remdesvir > Phenothrine> Casticin > Bergamottin > Ribavirin > Lacidipine; thus, the conformation of the ligand in the active gouge of the receptor (3MWP) indicated that Remdesvir, Phenothrine, Casticin, and Bergamottin are more active inhibitors against 3MWP.

Therefore, botanical drugs (Casticin and Bergamottin) could serve as inhibitors against 3MWP, although Remdesvir and Phenothrine could be more potent.

FIG. 1: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 3MWP

Docking with 3MWT: Binding mode and scoring of these drugs (Bergamottin, Casticin, Lacidipine, Phenothrin, Remdesvir, and Ribavirin) with 3MWT receptor showed that all the drugs showed that Remdesvir also has the lowest binding affinity of -9.8 kcal/mol.

TABLE 2: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 3MWT RECEPTOR WITH THE LIGANDS

The binding affinities predicted are -7.4 kcal/mol for Lacidipine, -6.9 kcal/mol for Casticin, -6.6 kcal/mol for Ribavirin, -5.7 kcal/mol for Phenothrin and Bergamottin  with-5.1 kcal/mol Table 2. The inhibition constant (Ki) of the drugs ranges from 0.07 – 181.80µM with Remdesvir having 0.07 µM and Bergamottin 181.80 µM. The H bond and other hydrophobic interactions showed that Casticin formed H bond with ARG'492, ARG'492, ASP'533, GLU'391, GLU'391, ILE'390, GLN'425 and ASP'426; and hydrophobic interactions with GLN'422, ARG'393, SER'430, GLY'392, ASP'389, PHE'537, LYS'488, HIS'528 and TYR'429. Lacidipine formed H bond with GLY'249, TYR'213 and GLU'219; Ribavirin with PHE'176, GLN'175, ASN'174, GLU'117, GLU'117 and ARG'323; Remdesvir with ASN'240, SER'238, ASN'305, ASN'305 and SER'238; Bergamottin with ARG'59 and ASN'240. Phenothrin only showed hydrophobic interactions with LEU'140, ALA'139, GLN'136, ARG'137, GLN'133, LYS'374, LEU'378, MET'371, ASP'375 and ARG'115 Table 2 and Fig. 2.

FIG. 2: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 3MWT

The ordering of the affinity of these drugs 3MWT are Remdesvir >Lacidipine > Casticin >Ribavirin > Phenothrin > Bergamottin. This showed that Casticin could inhibit 3MWT, but Remdesvir and Lacidipine are more active inhibitors against 3MWT.

Docking with 3MX2: The superlative conformation of the drugs with 3MX2 showed that Bergamottin, Casticin, Lacidipine, Phenothrin, Remdesvir and Ribavirin have the lowest binding affinities of -6.0, -8.5, -7.8, -6.6, -10.5 and -6.2 kcal with inhibitory constant (Ki) 39.72, 0.58, 1.90, 14.44, 0.02 and 17.10 µM respectively Table 3. The ordering of the score values for these drugs with 3MX2 receptor is as: Remdesvir > Casticin > Lacidipine > Phenothrin > Bergamottin >.

TABLE 3: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 3MX2 WITH THE LIGANDS

The 3MX2 residues in the binging gorge; ASP'451, ARG'455, LEU'453, MET'377, PRO'454, GLN'133, GLN'136, GLN'132, LEU'378, LYS'374, ASP'375 and ALA'452 formed hydrophobic interactions with Bergamottin, as well as H bond with ARG'137.

Lacidipine formed H bond with ALA'552, LEU'550, ALA'169, ASN'168, GLU'170 and GLU'170; Ribavirin displayed H bond interaction with TYR'319, TYR'209, ASN'305, TYR'209 and GLU'266; Remdesvir showed H bond with ASN'173, ARG'329, ARG'329, GLU'117, LEU'550, ALA'552 andARG'118; Casticin showed H bond with THR'178, GLY'249, GLU'266 and TYR'209.

Phenothrin only showed hydrophobic interactions with THR'13, PRO'302, ASN'305, TYR'209, ARG'300, THR'234, LEU'248, PRO'214, ASN'215 and TYR'213 Table 3 and Fig. 3. This showed that Remdesvir, Casticin and Lacidipine are more active against 3MX2 than others drugs.

FIG. 3: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 3MX2

Docking against 3MX5: Conformational interactions of the drugs with 3MX5 are displayed in Table 4 and Fig. 4, the data from Table 4 showed that the binding affinities predicted are -8.5 kcal/mol for Casticin, -8.4 kcal/mol for Lacidipine, -6.6 kcal/mol for Phenothrin, -6.5 kcal/mol for Ribavirin, - 10.1 kcal for Remdesvir and -8.1 kcal/mol for Bergamottin. The affinity ordered as Remdesvir > Casticin > Lacidipine > Bergamottin > Phenothrin > Ribavirin. Thus, it seemed that Remdesvir and Casticin are most active against 3MX5. The H bond and hydrophobic interactions of 3MX5 receptor with the drugs are shown in Fig. 4. Remdesvir formed H bond with ASN'305, GLU'117, LYS'309, ARG'323, PHE'176, THR'178, LYS'253 andLYS'309; Bergamottin displayed H bond interaction with GLY'298 and SER'238; Ribavirin formed H bond with ARG'329, GLU'117, ARG'323, ASN'240, PHE'176, GLY'117, PHE'176 and ILE'241; Casticin showed H bond with TRP'164 and hydrophobic interactions with LEU'172, SER'121, PHE'176, LEU'120, GLY'177, ARG'300, ARG'323, LYS'253, THR'178, ASN'305, LYS'309, SER'238, LEU'239, THR'116, ILE'241, GLU'117, MET'54, ASN'240 and ARG'59. Also, Lacidipine has H bond pose with ARG'300 and GLU'299, but hydrophobic interactions with LEU'248, SER'237, TYR'213, GLY'249, SER'9, PHE'10, THR'13, LEU'265, TYR'209, LYS'253, GLU'266, TYR'319, ASN'305, ASN'301, PRO'302 and SER'238; whereas Phenothrin displayed H bond with GLU'266 and hydrophobic interactions withARG'300, ASN'301, SER'238, GLY'249, LYS'253, LYS'309, TYR'319, LEU'265, ASN'305, TYR'209, THR'13, TYR'213, PRO'302, PHE'10 and SER'9.

TABLE 4: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 3MX5 WITH THE LIGANDS

FIG. 4: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 3MX5

Docking with 3T5N: Docking results of theseselected drugs with 3T5N are presented in Table 5 and Fig. 5. The binding energies of the Bergamottin, Casticin, Lacidipine, Phenothrin, Remdesvir and Ribavirin are -8.2, -7.5, -7.1, -6.9, - 8.7 and -6.2 kcal/mol with corresponding inhibitory constant (Ki) of 0.97, 6.21, 8.70, 0.42 and 28.37 µM respectively. This showed that Remdesvir and Bergamottin were presented with lowest binding affinity (i.e higher activity, 0.42 and 0.97 µM respectively); Lacidipine and have similar scoring affinity with 3T5N receptor. The binding affinity is ordered as Remdesvir > Bergamottin > Casticin > Lacidipine > Phenothrin > Ribavirin. Remdesvir formed H bond with ARG'300, ASN'240, ARG'329, ASN'174, GLY'177 and ARG'323; it also interacted hydrophobically withTYR'308, LYS'112,LEU'109, LYS'309, LYUS'253, THR'178, PHE'176, GLN'175, TRP'164, LEU'172, SER'172 and LEU'312. Bergamottin formed H-bond with ARG'323, LYS'309, ASN'174, ARG'329 and LEU'172; and hydrophobic interactions with PRO'297, LYS'112, LEU'109, TRP'331, SER'178, GLN'175, GLU'304, TYR'306, ARG'300, GLY'177 and LYS'258. Casticin is H bonded to GLY'309, LYS'253, ARG'323, ASN'174, LEU'172, PHE'176 and GLN'175; Lacidipine was H bonded to ARG'300, SER'9 and GLY'249; Ribavirin is H bonded to LYS'309, ARG'323, THR'178, LYS'253, PHE'176, GLN'175, ASN'174, ASN'174 and TYR'308, while Phenothrinis H bonded to GLU'266 Fig. 5. Therefore, Remdesvir and Bergamottin appeared as the most active against 3T5Q.

TABLE 5: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 3T5N WITH THE LIGANDS

FIG. 5: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 3T5N

Docking with 3T5Q: Docking of these drugs with 3T5Q revealed that Bergamottin, Casticin, Lacidipine, Phenothrin, Remdesvir and Ribavirin have binding affinity values of -7.1, -7.4, -7.4,-7.0, -9.2 and -5.8 kcal/mol, respectively; it is obvious that Remdesvir has the highest score with inhibitory constant (Ki) of 0.18 µM Table 6. Casticin and Lacidipine presented the affinity value, while that of Bergamottin and Phenothrin are quite similar in values but higher than Ribavirin. Remdesvir is H bonded to SER'247, THR'178, ARG'300, ARG'300, ARG'300, LYS'253, THR'178, ARG'323, ARG'323, ASN '174, LEU'172, PHE'176 andGLN'175, and interacted hydrophobically with GLY'249, ALA'250, GLY'177, LYS'309, SER'173, ASN'240, TRP'164, LEU'239, ARG'329, THR'308, LEU'109 and SER'238. Casticin is H bonded to ARG'300, ARG'300 and ARG'323, and it formed hydrophobic interactions with LYS'309, GLY'177, ASN'174, SER'173, LEU'172, PHE'176, ALA'179, LEU'312, TYR'308, ARG'300, ARG'329, ASN'240 and TRP'164. Bergamottin formed H bond with PRO'302 and TYR'209; Phenothrin has H bond pose with GLY'249 and Ribavirin is H-bonded to ASP'233, MET'231, PHE'246, ARG'55, ASN'245 and GLN'51as shown in Table 6 and Fig. 6.

TABLE 6: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 3T5Q WITH THE LIGANDS

FIG. 6: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 3T5Q

Docking against 4FVU: Docking mode analysis and binding affinity predicted for the drug-4FVU complex showed that the binding affinity of the most stable conformation of the drugs are -7.1, -6.9, -6.1, -5.2, -7.9 and -6.3 kcal/mol for Bergamottin, Casticin, Lacidipine, Phenothrine, Remdesvir and Ribavirin respectively; this showed that Remdesvir and Bergamottin are most active, affinity value of Casticin (-6.9 kcal) is similar to that of Bergamottin as shown in Table 7. Remdesvir formed H-bond with GLY'392, ASP'533, ARG'492, ARG'492, ARG'492, SER'491, ASP'389, GLN'462, ILE'390, ASP'466, GLY'463, ASP'426 and GLN'462, but interacted hydrophobically withGLU'515, ILE'525, LEU'486, SER'487, LYS'488, PHE'537, HIS'528, ARG'393, HIS'431, SER'430 and ALA'391. Bergamottin showed H-bond with HIS'412 and HIS'507, andhydrophobic interactions with ALA'440, ARG'556, ASP'437, PHE'560, VAL'559, TYR'410, PHE'414, LEU'505, TYS'506and MET'508. Casticin is  H-bonded to ASP'389, ILE'390, GLY'392, ARG'492 and GLN'462; Lacidipine is H-bonded to ARG'492, ARG'492, HIS'528, ASP'426 and ARG'393; Ribavirin formed H-bond with ARG'492, ASP'533, ASP'389, HIS'528, ILE'390, GLY'392, ASP'466, ASP'426 and ARG'393, where as Phenothrine is H-bonded to TYR'410 Fig. 7.

TABLE 7: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 4FVU WITH THE LIGANDS

FIG. 7: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 4FVU

Docking against 4GV9: The binding score energy results of the drugs toward 4GV9 protein showed that Bergamottin, Casticin, Lacidipine, Phenothrine, Remdesvir and Ribavirin have the binding score energy values of -6.7, -7.0, -6.5, -6.0, -7.7 and -6.2 kcal/mol, respectively as presented in Table 8. The binding affinity valves with 4GV9 for the drugs is ordered as Remdesvir >Casticin >Bergamottin >Lacidipine >Ribavirin > Phenothrine, this showed that Remdesvir and Casticin are active although the affinity values of Phenothrine and Ribavirin are similar.

Casticin is H-bonded to ARG'349, ARG'393, SER'430, ILE'390, GLU'391, ASP'533 and GLU'391, and having hydrophobic interactions with GLN'425, ASP'426, TYR'429, GLY'392, ASP'389, PHE'537, ARG'393, HIS'528, ARG'492 and LYS'488. Remdesvir formed H-bond with GLN'462, GLY'392, SER'430, GLY'392, GLU'391, ILE'390, ASP'533 and TYR'429, and hydrophobically with ASP'389, PRO'394, ARG'492, HIS'431, LYS'488, HIS'528, GLN'425, ARG'393, ASP'426, ASP'466, PHE'537 and GLY'463. Ribavirin is H-bonded to GLY'392, ASP'426, ASP'466, GLU'391, GLN'462, ILE'390, ASP'533, ASP'389 and GLU'391; Lacidipine is H-bonded to HIS'528, ARG'492 and GLU'391; Bergamottin is H-bonded to ASP'389, but has hydrophobic interactions with SER'487, SER'491, SER'430, ASP'533, PHE'537, LEU'486, ILE'390, ARG'492, LYS'488, GLN'462, GLU'391, ASP'466, GLY'392, GLY'463, ASP'465 and HIS'528. However, Phenothrine only exhibited hydrophobic interactions with PHE'537, SER'491, GLN'462, ARG'492, ASP'533, ASP'389, ILE'390, HIS'528, GLU'391, GLY'392, ARG'393, ASP'466, PRO'394, LYS'488, GLY'463 and SER'430.

TABLE 8: BINDING AFFINITY AND NON-BONDING INTERACTIONS OF 4GV9WITH THE LIGANDS

FIG. 8: THE BLIND DOCKED CONFORMATIONS OF INHIBITOR WITH 4GV9

ADME / Pharmacokinetic Predictions: Pharmacokinetic and toxic properties are imperative in drug safety assessment and also in the development of new drugs; these have made some drugs to be attrited at the trial stages and even for the approved drugs ⁴². Poor pharmacokinetics, solubility, and bioavailability have been linked to low drug potency, toxicity, and drug failure ^{43, 44}. Therefore the prediction of ADMET properties are considered to be an important step in order to reduce possible challenges that may come up later at the clinical trial treatments. ADME (absorption, distribution, metabolism, and excretion) properties, as well as drug-likeness analysis, are considered for study in this work to help rationalizing the quality/failure of inhibitors/drugs administration to a biological system ^{45, 46}. The Pfizer’s rule (Ro5) or Lipinski’s rule of five (5) by Christopher A. Lipinski in 1997 is a thumb rule for evaluating drug-likeness and to decide if an inhibitor with acertain biological and pharmacological properties could be orally active drug in the human body 47. In the is work, ADMET properties were predicted using online tools pkCSM ⁴⁸ and SwissADME 49 for two botanical drugs (Bergamottin and Casticin), and four synthetic drugs (Lacidipine, Phenothrine, Remdesvir, and Ribavirin) were evaluated for their pharmacokinetics and toxicity properties using in-silico approach. The rule states that a molecule or an inhibitor can be orally absorbed/active if two (2) or more of these thresholds; molecular weight (Mw) ≤ 500, octanol/water partition coefficient (iLOGP) ≤ 5, number of hydrogen bond acceptors (nHBA) ≤ 10, number of hydrogen bond donors (nHBD) ≤ 5, and topological polar surface area (TPSA) < 40 Ų). The drug-likeness parameters are related to aqueous solubility and intestinal permeability, which determines the first step of oral bioavailability ⁵⁰. The drug-likeness prediction showed that Bergamottin, Casticin, Lacidipine and Ribavirin have zero violation of the Lipinski’s rule except for Phenothrin and Remdesvir Table 9.

TABLE 9: DRUG LIKENESS OF THE LIGANDS

The drug-likeness parameters are related to aqueous solubility and intestinal permeability which determines the first step of oral bioavailability ⁵¹. The results in Table 10 also showed good pharmacokinetic properties in which Bergamottin, Casticin, Lacidipine and Phenothrin molecules have high gastrointestinal absorption while others have low GI absorption. P-gp inhibitors can affect or alter the pharmacokinetics properties of a drug ⁵², because P-gp molecules are present organs like BBB, bile ductule and kidney proximal tubule, so inhibition P-gp possibly increase the absorption, distribution, metabolism, and elimination of their substrates. Thus, it is very important to identify if a ligand is a substrate to Pgp (i.e. can be transported out of the cell) or inhibitor to Pgp (impair function). Lacidipine, Casticin and Remdesvir are predicted as both substrate, Bergamottin and Phenothrin as P-glycoprotein substrates and Ribavirin is neither P-glycoprotein substrate nor inhibitor.

Casticin, Lacidipine, Remdesvir, and Ribavirin possess blood-brain barrier BBB penetration except for Bergamottin and Phenothrin. The intestinal absorbance of the studied compounds is greater than 30%, indicating that all the combinations are highly absorbed through the intestine. However, Bergamottin, Casticin, Lacidipine and Phenothrin could be more absorbed than Remdesvir and Ribavirin Table 10. Therefore, Bergamottin and Casticin of botanical origin can be more absorbed easily be absorbed through the intestinal wall than Remdesvir and Ribavirin ⁵³. The Brain Or Intestinal Estimate D permeation predictive model (BOILED-Egg), also known as Egan egg graph of the drugs were generated from SwissADME online web server which revealed a clear graphical representation of the absorption of the molecules in the brain and gastrointestinal tract ⁴⁸. The graph molecules in the yolk area (yellow) are predicted to inactively permeate the blood-brain barrier (Bergamottin and Phenothrin), while Bergamottin, Casticin, Lacidipine and Phenothrin are predicted to be highly absorbed in the gastrointestinal tract Fig. 9. These theoretical findings are in agreement with the experimentally pharmacokinetic profilereported ⁵⁰.

Likewise, the bioavailability radar shows a rapid appraisal of the drug-likeness of a molecule by taking six (6) physicochemical properties into consideration: saturation, lipophilicity, polarity, size, solubility, and flexibility ⁵¹.

Fig. 10 shows the bioavailability radars of the drugs in which the molecules are predicted to be orally bioavailable (low flexibility and polarity), less toxic, and good absorption.

All the compounds are not toxic as predicted by AMES test, this is very crucial since the safety parameter is important to the development of a successful drug ⁵².

Inhibition of cytochrome P450 isoforms can lead to drug-drug interactions in which co-administered drugs fail to be metabolized, thereby can accumulate to toxic levels ⁵⁴ some of the drugs can inhibit the cytochrome P450 isoforms with exception of Remdesvir and Ribavirin Table 10.

TABLE 10: ADMET PROFILE OF THE STUDIED DRUGS

FIG. 9: BOILED-EGG GRAPH OF THE IPA MOLECULES

FIG. 10: BIOAVAILABILITY RADAR OF THE BOTANICAL DRUGS (BERGAMOTTIN AND CASTICIN) AND COMMERCIALLY APPROVED DRUGS

CONCLUSION: The purpose of this study is to gauge the binding affinity of the botanical drugs (Casticin and Bergamottin) with some selected antiviral drugs ((Lacidipine, Phenothrine, Remdesvir and Ribavirin) being administered for the treatment of patients with Lassa fever.

The results showed that Remdesvir, Phenothrin and Casticin are more active against 3MWP; Remdesvir, Lacidipine and Casticin are active against 3MWT, 3MX5 and 3T5Q; Remdesvir, Bergamottin and Casticin against 3T5N; Remdesvir, Casticin and Bergamottin showed more inhibitory action against 4FVU. Generally, Remdesvir showed outstanding inhibitory action against nucleoprotein (NP) of the Lassa virus, NP for the RNA synthesis and immune suppression, NP for the genomic ribonucloeprotein complexes, NP exonuclease activity causes suppression of innate immune signaling the infected cell, and 3’-5’ exoribonuclease  suppresses type 1 interferon (IFN).

Also Casticin, a botanical drug showed very good activity against a number of nucleoproteins (NP) of the Lassa virus than Bergamottin, thus could be used to treat Lassa fever. ADMET profile revealed that Bergamottin, Casticin, Lacidipine and Phenothrin could be readily absorbed than Remdesvir and Ribavirin into intestinal wall; therefore, Bergamottin and Casticin of botanical origin can easily be absorbed through intestinal wall than Remdesvir and Ribavirin. All the drugs can inhibit the cytochrome P450 isoformsin except Remdesvir and Ribavirin.

Research Funding: The authors received no funding for this work.

ACKNOWLEDGEMENT: The authors are grateful to the Department of Pure and Applied Chemistry for the computational resources

CONFLICT OF INTEREST: The authors have no conflict of interest.

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    How to cite this article:

    Omotayo IA, John AA, Gbenga OO, Misbaudeen A, Felix LD, Kolawole OA and Banjo S: In-silico assessment via molecular docking and admet profile of botanical drugs (Bergamottin and Casticin) against trial drugs for lassa virus. Int J Pharm Sci & Res 2022; 13(9): 3494-18. doi: 10.13040/IJPSR.0975-8232.13(9).3494-18.

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