View of Molecular Docking and Interaction Analysis of Propolis Compounds Against SARS-CoV-2 Receptor

(1)

JOURNAL OF TROPICAL LIFE SCIENCE

2022, Vol. 12, No. 2, 219 – 230 http://dx.doi.org/10.11594/jtls.12.02.08

How to cite:

Syaban MFR, Faratisha IFD, Yunita KC, et.al., (2022) Molecular Docking and Interaction Analysis of Propolis Compounds Research Article

Molecular Docking and Interaction Analysis of Propolis Compounds Against SARS-CoV-2 Receptor

Mokhamad Fahmi Rizki Syaban *, Icha Farihah Deniyati Faratisha, Khadijah Cahya Yunita, Nabila Erina Erwan, Dedy Budi Kurniawan, Gumilar Fardhani Ami Putra

Department of Biomedicine, Faculty of Medicine, Brawijaya University, Malang, 65111, East Java, Indonesia

Article history:

Submission September 2021 Revised September 2021 Accepted December 2021

ABSTRACT

Herbal medicine is a conventional medicinal option for many people, particularly in developing countries, to cure diseases, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Propolis is one of the popular herbal medicine which has various health benefits, particularly antiviral activity. In this molecular docking study, our investigation examined 25 kinds of Propolis to bind SARS-CoV-2 protein with the main targets of ACE-2 and M^Proreceptors. Propolis ligands were downloaded from PubChem, ACE-2, and M^Pro receptors from Protein Data Bank. Both ligands and targets were optimized by PyMOL. The pharmacokinetics and toxicity analysis was conducted using OSIRIS software. Molecular docking was done using PyRx 0.9, and its binding interaction was visualized by Discovery Studio. There were two compounds with the strongest interactions with ACE-2 and MPro receptors: Kaemferol and Abietic acid. Pharmacokinetic analysis revealed that these drugs have good pharmacokinetic properties. However, the findings of toxicity tests indicated that Kaempferol has the potential to be mutagenic. Kaempferol and Abietic acid compounds bind to M^proand ACE-2 receptors and could be used to treat SARS-CoV 2 infection. However, further study on the efficacy and toxicity of this compound is required before it may be administered to humans.

Keywords:ACE-2 receptor, COVID-19, Main protease, Molecular docking, Propolis, SARS-CoV-2

*Corresponding author:

E-mail: mokhamad- fahmi@gmail.com

Introduction

The pandemic of coronavirus disease 2019 (COVID-19) caused by the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) is a severe problem affecting the whole world.

The virus, naturally easily transmitted, has spread to 210 countries in just four months since it was first identified at the end of 2019. COVID-19 can infect several organs, such as the lungs, liver, and digestive system. To date, there is no adequate management for overcoming COVID-19 [1–3].

Meanwhile, angiotensin-converting enzyme 2 (ACE-2) is a receptor in the human body against the COVID-19 virus. The complete gene sequence of the COVID-19 virus, which shows similarities to the spike protein in SARS-CoV-1, is strong evidence that it uses ACE-1 as its receptor. Structural studies also show that the protein spike in COVID-

19 binds to ACE-2 in an affinity ten to twenty times higher than SARS-CoV-1. In-vivo evidence with ACE-2 transgenic mice revealed that it can be infected with the virus and induce interstitial pneumonia. The high affinity of the COVID-19 virus for ACE-2 can be transmitted between humans [4–6].

Studies showed increased ACE-2 expression in animals administrated with ACE-Inhibitor (ACEI) and angiotensin receptor blocker (ARB) [7]. This could theoretically increase the risk of SARS-CoV-2 infection since the ACE-2 receptor is one of its ways to bind to host cells. Second, the role of ACE-2 in converting Ang II to Ang-(1-7).

The imbalance between Ang II and Ang-(1-7) could lead to acute lung injury and pulmonary fi-

(2)

JTLS | Journal of Tropical Life Science 220 Volume 12 | Number 2 | May | 2022

brosis. In hypertensive patients, treatment with either ACEI or ARB led to increased expression of ACE-2, which impairs balance between Ang II and Ang-(1-7), leading to Ang-(1-7) driven acute lung injury and pulmonary fibrosis [8]. With our findings regarding the ability of propolis compounds to bind to ACE-2 receptor, propolis could be a potential preventive or therapeutic natural product for hypertensive people with COVID-19 treated with either ACEI or ARB regarding the possibility of Ang-(1-7) mediated acute lung injury and pulmonary fibrosis.

On the other hand, the main protease (M^pro), papain-like protease (PLP) or commonly known as 3CL protease (3CLpro), plays an essential role in cutting pp1a and pp1ab polyproteins in coro- nary viruses into non-structural functional proteins. M^pro, which consists of 300 amino acids and three domains, is relatively the same in various coronavirus species. There is also no homolog of M^pro in the human body. Given the critical role of M^proin viral gene replication and transcription, it makes M^pro an ideal target for antivirals because the inhibition of these proteases can block the replication, transcription, and proliferation of viruses [9–11].

Natural products are starting to be considered an alternative to the existing drugs, given the pro- blems that can arise from them, such as drug re- sistance and side effects. Humans have used natural products from plants and their derivatives to fight disease as prevention or adjuvant therapy [12, 13]. In honey, propolis is a natural product from bees that have been studied extensively regarding their biological mechanisms and their benefits on human health. Propolis and its extracts have various health benefits because they have an- tibacterial, antioxidant, anti-inflammatory, and immunomodulatory properties [14].

The complexity of Propolis is contained in its chemical composition. The composition of propolis has a different variability based on seasons, bee species, availability of plants and plants around the beehive, and altitude [15]. The main compounds of propolis known are aromatic acids, fla- vonoids, diterpenoid acids, phenolic compounds, and triterpenoids [16]. The diversity of these compounds can be used as potential drugs with effects that need to be explored further. The mechanism of action from this compound consists of blocking the possibility of virus transmission to other cells,

inhibiting its spread, and destroying the viral en- velope [17].

Additionally, molecular docking is a molecular screening study of drugs to determine an effect when a compound interacts with a target protein.

Screening a compound helps researchers look for compounds as the drug candidates for disease [18, 19]. For this reason, this investigation conducted a screening test of compounds contained in Propolis as the drug candidates against SARS-CoV-2 infection.

Material and Methods Ligands Search

Ligands derived from Propolis were obtained from the previous research journal literature studies. The selected literature study of phytochemi- cal substances from Propolis was ge-nerated from various regions in Indonesia. The compounds contained in Propolis were acquired from the results of a literature search using the Google Scholar search engine, NCBI, Sciendi-rect, used the key- word of “Propolis", "active compound", "Antivi- ral", and "Indonesia". Ligands that were not found in the PubChem or ChemSpider databases were excluded.

Ligands and Protein Receptor Preparation The 3D structure of Propolis compounds was downloaded from PubChem (https://pubchem.ncbi.nlm.nih.gov/) or ChemSpider (http://www.- chemspider.com/) and then saved in SDF format.

Furthermore, the test ligand compound's energy was minimized to obtain an ideal binding inte-rac- tion strength using OpenBabel. The target pro-tein of Angiotensin-Converting Enzyme 2 (PDB ID:

1R4L) and SARS COV-2 Main Protease (PDB ID:

6LU7) were downloaded from the Protein Data Bank (www.rscb.org) and then optimized using PyMOL by removing the existing residues such as water, ligands from crystallization, and co-factors.

The structure was saved in the form of PDB. We also used control ligands were com-pounds of XX5 a (ChemID 395128) and PRD_00-2214 (ChemID 4883311). The control ligands and protein targets were chosen based on previous studies related to the exploration of natural compounds for COVID-19 [20].

(3)

Pharmacokinetic Profile

The tested ligand compounds were analyzed for pharmacokinetic profiles using SwissADME (http://www.swissadme.ch/index.php) by entering the SMILES formula of each active substance as seen in Table 1. Lipinski Rule of Five (LR5) analysis was carried out to assess the pharmaco-kinetic ability of the compound [21, 22]. LR5 criteria in which if any compound meets these, it can be cat- egorized as a drug.

Visualization of Specific Docking

The computational molecular method (Com- putational Docking) was performed to see the ligand's possible orientation and conformation at

the protein binding sites. This examination did a specific docking at the active site of the target.

Molecular docking was done using a personal computer with specifications windows 10, 16GB RAM, SSD 210, and a Ryzen 5 2400U processor.

Molecular docking was performed using a personal computer that ran Windows 10, had 16GB of RAM, a 210GB SSD, and a Ryzen 5 2400U processor. Molecular docking was perfor-med on a specific site, and grid box dimensions were established by fixing x, y, and z. The dimensions of the grid box ACE-2 and M^pro are based on a previous study, as shown in Table 2 [20]. The complex ligands with the receptor were then analyzed for their Table 1. Active Compound of Propolis

No. Compound PubCID Cannonical SMILES

1. Abietic Acid 10569 CC(C)C1=CC2=CCC3C(C2CC1)(CCCC3(C)C(=O

)O)C

2. Patchoulene 91746471 CC1CCC2=C1CC3CCC2(C3(C)C)C

3. 3,4-dimethylthioquinoline 613533 CSC1=C(C2=CC=CC=C2N=C1)SC

4. Acacetine 5280442 COC1=CC=C(C=C1)C2=CC(=O)C3=C(C=C(C=C

3O2)O)O

5. Galangin 5281616 C1=CC=C(C=C1)C2=C(C(=O)C3=C(C=C(C=C3O

2)O)O)O

6. Kaempferol 5280863 C1=CC(=CC=C1C2=C(C(=O)C3=C(C=C(C=C3O

2)O)O)O)O

7. Chrysin 5281607 C1=CC=C(C=C1)C2=CC(=O)C3=C(C=C(C=C3O

2)O)O

8. Benzoic acid 243 C1=CC=C(C=C1)C(=O)O

9. Phenylic acid 996 C1=CC=C(C=C1)O

10. D-glucofuranuronic acid 441478 OC(C1OC(C(C1O)O)O)C(=O)O

11. Bis(2-ethylhexyl) phthalate 8343 CCCCC(CC)COC(=O)C1=CC=CC=C1C(=O)OCC (CC)CCCC

12. 1-Heptacosanol 74822 CCCCCCCCCCCCCCCCCCCCCCCCCCCO

13. Nonacosane 12409 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC

14. Pentatriacontane 12413 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

CCCC

15. Hexadecanoic Acid 985 CCCCCCCCCCCCCCCC(=O)O

16 Hexadecane 11006 CCCCCCCCCCCCCCCC

17 Hexadecanol 2682 CCCCCCCCCCCCCCCCO

18 Butone 4781 CCCCC1C(=O)N(N(C1=O)C2=CC=CC=C2)C3=C

C=CC=C3

19 Hepatacosane 11636 CCCCCCCCCCCCCCCCCCCCCCCCCCC

20 Limonene 22311 CC1=CCC(CC1)C(=C)C

21 Ocatadecane 11635 CCCCCCCCCCCCCCCCCC

22 Phenol 996 C1=CC=C(C=C1)O

23 Tricosane 12534 CCCCCCCCCCCCCCCCCCCCCCC

24 9-Octadecen-1-ol 8927 CCCCCCCCC=CCCCCCCCCO

25 Dioctyl adipate 31271 CCCCCCCCOC(=O)CCCCC(=O)OCCCCCCCC

(4)

interaction visualization using the Discovery Stu- dio software.

Results and Discussion

Active compounds in Propolis were downloaded from PubChem (http://pubchem.ncbi.nlm.- nih.gov/) in sdf format. The analyzes of these compounds were accomplished according to LR5 (Table 3). LR5 is a criterion used as one of the guidelines in assessing a compound similar to a drug. These criteria include hydrogen bond acceptor (HBA) < 10, hydrogen bond donor (HBD) < 5, molecular weight < 500 Dalton, H2O partition co- efficient (logP) < 5, and molar refractivity between 40-130. Compounds that comply with LR5 have good pharmacokinetics [23].

Moreover, this examination revealed that the average active compounds contained in propolis met LR5 criteria. Thus, it had good pharmacokinetics. However, some compounds such as Octa- decane, Hepatocosane, Tricosane, and Dioctyl

adipate do not meet LR5 criteria because they have a high logP. Lipophilicity, also known as the LogP, is a molecule property that indicates the ra- tio of the concentration of a compound between two phases, often oil and liquid phase, at equilib- rium [24]. Physicochemical parameter lipophilicity has to be considered while designing novel medications because it has been shown to substan- tially impact different pharmacokinetic character- istics such as absorption, distribution, permeabil- ity, and the routes of drug clearance [25, 26].

Then, using computer analysis and software applications, compounds comparable to the drug were studied further to identify the type of interaction with target proteins.

Meanwhile, the molecular docking study is a research model used for drug discovery to determine the binding interaction between ligand-protein [27, 28]. This study was specific because the functional domain of the target protein was known. The functional domains of M^pro and ACE- Table 2. Protein structure of M^Proand ACE-2

No. Protein PDB ID 2D Grid Center Grid Box

Size(A^o)

X Y Z

1. ACE-2 1R4L 45.27 8.21 32.65 30 x 30 x 30

2. M^Pro 6LU7 -12.71 17.14 65.92 30 x 30 x 30

Table 3. Pharmacokinetic analyses of propolis constituent

No. Chem compound Molecule

Mass

Acceptor H Donor H LogP Lipinski

1 Abietic Acid 302.45 2 1 4.37 Yes

2 Patchoulene 204.35 0 0 4.40 Yes

3 3,4-dimethylthio Quinoline

221.34 1 0 3.19 Yes

4. Acacetin 284.26 5 2 2.52 Yes

5. Galangin 270.24 5 3 1.99 Yes

6. Kaempferol 286.24 6 4 1.58 Yes

7. Chrysin 254.24 4 2 2.55 Yes

8. Benzoic acid 122.12 2 1 1. 44 Yes

9. Phenylic acid 94.11 1 1 1.1 Yes

10. D-glucofuranuronic acid 194.14 7 5 -2.16 Yes

11. Bis(2-ethylhexyl) phthalate 390.56 4 0 6.17 Yes

12. 1-Heptacosanol 396.73 1 1 9.43 Yes

13. Nonacosane 408.79 0 0 11.18 Yes

14. Pentatriacontane 492.95 0 0 13.33 Yes

15. Hexadecanoic Acid 256.42 2 1 5.20 Yes

16. Hexadecane 226.44 0 0 6.42 No

17. Hexadecanol 242.44 1 1 5.42 Yes

18. Butone 44.10 0 0 1.54 Yes

19. Hepatacosane 380.73 0 0 10.46 No

20. Limonene 136.23 0 0 3.37 Yes

21. Octadecane 254.49 0 0 7.18 No

22. Phenol 94.11 1 1 1.41 Yes

23. Tricosane 324.63 0 0 9 No

24. 9-Octadecen-1-ol 268.48 1 1 5.8 Yes

25. Dioctyl adipate 470.57 4 0 6.14 No

(5)

2 target proteins were in the grid box presented in Table 2. Docking was performed with PyRx,

PyMOL, and Discovery Studio software, resulting in the interaction energy and interaction between Table 4. Binding affinity and amino acid residue interaction conformation from propolis constituent with ACE-

2 Receptor and M^pro Ligand

Type No. Ligand Name

ACE-2 M^pro

Binding Affinity (kcal/mol)

Amino Acid Resi- due

Binding Af- finity

(kcal/mol) Amino Acid Residue Control 1. XX5 -9.2 Hydrogen bond:

Arg273, Pro346 Ikatan Hydropho- bic: Tyr515, Thr347, Phe504, His505, His345, Glu375, His378, Tyr510, Glu402, Thr371, His374 2. PRD_00

2214 -7.8 Hydrogen Bond: Tyr54,

Glu166, Gln189

Hydrophobic Bond:

Thr190, Met165, His164, Met49, Asp187, His41, Arg188, Cys145, His163, Asn142, Leu27, Phe140, Thr26, Ser144, Gly143, Leu141, Pro168 Natural

Com- pound

1 Abietic Acid

-9.0 Hydrophobic bond:

His345, Phe274

-7.5 Hydrogen bond: Leu141, His163, His173

2 Patchou-

lene -6.9 Hydrophobic bond:

Phe274, His374 -5.1 Hydrophobic bond:

His41, Cys145 3 3,4-di-

methyl- thio quinoline

-6.2 Hydrophobic bond:

Phe274, His374 -5.0 Hydrophobic bond:

His41, Met49, Met165 4. Acacetin -8.6 Hydrogen bond:

Arg273, Glu402, Arg518, Tyr515 Hydrophobic bond:

Arg273, Phe274, His374, Glu375, Glu406, Tyr515 Unfavorable acceptor-acceptor:

His374

-7.5 Hydrogen bond: Leu141, Cys145, His163, Glu166 Hydrophobic bond:

Met165, Pro168 Unfavorable acceptor- acceptor: Gly143

5. Galangin -9.0 Hydrogen bond:

His345, Glu402 Hydrophobic bond:

Arg273, Pro346, Glu375, Tyr510

-7.3 Hydrogen bond: Cys145, His163 Hydrophobic bond: Cys145

6. Kaempfe

rol -8.8 Hydrogen bond : His345, Glu402, Tyr510, Tyr515, Arg518

Hydrophobic bond:

Arg271, Pro346, Glu375, Tyr510

-7.8 Hydrogen bond: Glu166 Hydrophobic bond:

Cys145, His41, Met165, Met49

Continue

(6)

JTLS | Journal of Tropical Life Science 224 Volume 12 | Number 2 | May | 2022 Ligand

ACE-2 M^pro

Binding Af- finity

(kcal/mol) Amino Acid Residue 7. Chrysin -8.9 Hydrogen bond :

Pro346, His374 Hydrophobic bond:

Arg273, Phe274 Glu375

-7.2 Hydrogen bond: Phe140, Cys145 Hydrophobic bond: Leu27, His41, Cys145

8. Benzoic acid

-5.8 Hydrogen bond : His345, Ser128, Tyr127

Hydrophobic Bond:

Cys344, Leu144, Leu143

-4.6 Hydrogen bond: Tyr54, Arg188

Hydrophobic bond:

Met165, Met49 9. Phenylic

acid -4.7 Hydrogen bond:

Arg514

Hydrophobic bond:

Tyr510

-3.9 Hydrogen bond: Tyr54 Hydrophobic bond:

Met165, Met49

Unfavorable acceptor- acceptor: Asp187 10. D-gluco-

furanuro nic acid

-6.3 Hydrogen bond:

His378, Arg273, His505, His345, Glu375, Pro346 Unfavorable acceptor-acceptor:

Glu402

-5.3 Hydrogen bond: Gly143, Leu141

Unfavorable acceptor-acceptor: Asn142

11. Bis(2- ethylhex yl) phthalate

-6,9 Hydrogen bond:

Arg273, Tyr127, His345

Hydrophobic bond:

Cys344, Pro346

-5,7 Hyd 5rogen bond:

Gly143, Cys 145 Hydrophobic bond:

His41, Met165 Pi-Sulfur: Met49 12. 1-Hepta-

cosanol -5,3 Hydrophobic bond:

Trp271, Phe274, His345, Pro346, His374

-4,2 Hydrogen bond:

Gly143

Hydrophobic bond:

Cys145, His163, Met165, Pro168

13. Nonaco-

sane -5,9 Hydrophobic bond:

Leu143, Leu144, Cys344, Tyr127, His345, Pro346, Lys363, Phe274

-4,1 Hydrophobic bond:

Cys145, His41, His 163, Pro168, Met165 14. Pentatri-

acontane

His374, Pro346, Trp271, Phe274, Ala153

Leu27, His41, Met49, Cys145, His163, Met165 15. Hexadec-

anoic Acid

-5,8 Hydrogen bond:

Ser409, Thr371 Hydrophobic bond:

His345, Pro346, Phe274

-4,2 Hydrogen bond:

His41

Hydrophobic bond:

Cys145, His163 16. Hexade-

cane -4.9 Hydrophobic bond:

Trp271,Arg273, Phe274, His345

His41, Met49, Cys145, His163

17. Hexa- decanol

-5.5 Hydrogen bond:

Thr129

Hydrophobic bond:

-4.3 Hydrogen bond:

Thr190, Gln192 Hydrophobic bond :

Continue

(7)

JTLS | Journal of Tropical Life Science 225 Volume 12 | Number 2 | May | 2022 Ligand

ACE-2 M^pro

Binding Af- finity (kcal/mol)

Amino Acid Residue Tyr127, Leu144,

Trp271, Cys344, His345, Phe274

His41, Met49, Met165 18. Butone -3.8 Hydrogen bond:

Ser128, Cys344, His345

Hydrophobic bond:

Tyr127, Leu144

-3.1 Hydrogen bond : Asp187

Hydrophobic bond : Met49

19. Hepata- cosane

Trp271, Phe274, Cys344, His345, Pro346

His41, Met49, Leu27, Cys145, His163, Met165 20. Limo-

nene -5.8 Hydrophobic bond:

Leu370, Phe274 -4.4 Hydrophobic bond:

His41, Met49, Met165 21. Octade-

cane

Leu144, Tyr127, Leu143, Trp271, Cys344, His345, Pro346

Leu27, His41, Met49, Cys145, Met165

22. Phenol -4.7 Hydrogen bond:

Tyr127, Leu144 Hydrophobic bond:

Leu143

His41, Met49 23. Tri-

cosane -6.5 Hydrogen bond:

Arg273, Tyr515 Hydrophobic bond:

Ala153, Trp271, Phe274, Pro364, His374

-4.2 Hydrogen bond:

His41, Cys145, His163, Met165

24. 9-Octa- decen-1- ol

-6.8 Hydrogen bond:

His345, His505 Hydrophobic bond:

Tyr127, Leu144, Ala153, Trp271, Pro346

-6.5 Hydrogen bond: Arg 273, Tyr 515

Hydrophobic bond:

Ala153, Trp271, Phe274, Pro346, His374

25. Dioctyl adipate

-6.3 Hydrogen bond:

Arg273, His345, Glu406 His505, Arg518

Hydrophobic bond:

Phe274, His378, Phe504, Tyr510

-4.8 Hydrogen bond:

Glu166, His163, His172 Hydrophobic bond : Leu27, His41, Cys145, Met165

Notes: XX5 = ACE-2 inhibitor bound, PRD_002214 = irreversible peptide-like inhibitor of the main protease (M^Pro)

the ligand and the target protein [28, 29]. After the results obtained in the study, the analysis of the binding energy was completed, and it displayed that none of the active compounds of Propolis had binding energy more excellent than the control.

However, Kaempferol had the same binding energy when compared to the control. Specifically,

Kaempferol had binding energy at the value of 7.8 Kcal/mol, the same as PRD_002214 as the control ligand of M^pro. The Abietic acid compound had the highest average strength with ACE-2 and M^pro when compared to other substances. Abetacid has a binding affinity for ACE-2 and M^Pro of -9.0 kcal/mol and 7.5 kcal/mol, respectively (Table 4).

(8)

The assessment of overall toxicity is a critical parameter in determining whether a compound is hazardous or safe for humans. Predictions of hazardous parameters are made with the help of the OSIRIS program. Toxicity tests conducted on animals in a wet lab are regarded to be time-consum- ing and expensive. Therefore, computer prediction for toxicity of the molecule has been extensively explored without the need for costly animal testing [30]. The OSIRIS program is used to compute the toxicity prediction done for muta-genic impact, tumorigenic effect, reproductive effect, and irritat- ing effects. No risk (1.0), medium risk (0.8), and high risk (1.0) are the three different categories of risks (0.6). If the value decreases to less than one, the molecule's toxicity increases, and the substance is no longer regarded as a medicine. Kaem- pferol has a mutagenic effect in terms of toxicity.

However, abietic acid has good safety and tolera- bility profiles. The assessment toxicity risk of

Propolis compounds can be seen in Table 5. Alt- hough it demonstrates a significant risk, which is constantly dependent on the quan-tity, more wet- lab investigations are necessary for toxicity evalu- ation and dose optimization. As a result, a lower quantity will always have the same effect as a drug [30, 31].

Additionally, the analysis of the types of bond interaction between kaempferol and abietic acid with target protein was performed and compared to the amino acid residues formed with the control ligand. The visualization of ACE receptor-ligand complex interactions can be seen in Figure 1.

Meanwhile, the types of interaction formed from M^proreceptor-ligand are shown in Figure 2. The type of bond formed from the interaction between Kaempferol and M^pro, which has a hydrogen bond on the amino acid Glu166, and hydrophobic bonds with amino acid residues like Cys145, His41, Met165, Met49. Compared to the control, the Table 5. Toxicity risk of propolis compound

Compound Mutagenic Tumorigenic Irritant Reproductive Effect

Abietic Acid 1 1 1 1

Kaempferol 0.6 1 1 1

Notes: 1= no risk; 0.8=medium risk; 0.6=high risk

Figure 2. Visualization of M^Pro-ligand complex interactions with ligands. (A) Abietic Acid (Yellow stick) and (B) Kaempferol (Cyan stick)

(9)

amino acid residues formed have similarities with Glu166 (hydrogen bonds), Cys145, His41, and Met165 (hydrophobic bonds). Therefore, Abietic acid has the same residual binding as the control ligand. Abietic acid binds to the ACE-2 receptor in the same amino acid in His345, and the M^Pro receptor in Leu141 and His163.

Furthermore, the similarity of the bonds will produce the same function as the control ligand; in this case, kaempferol can inhibit the action of M^pro. The strong protein-ligand bonds can affect a target protein's biological activity. Thus, this compound is predicted to have activity in hindering M^pro[29].

By inhibiting the M^Pro activity, kaempferol can in- terfere with the proteolytic function of the M^pro protein, which is essential for viral replication and the pathogenesis of COVID-19. Inhibition prediction can be ascertained by the interaction with the amino acid residue of the control ligand in this study and similarly such in SARS-CoV-2 M^Pro and N3 inhibitor molecular docking analysis specifically in the catalytic dyad (Cys145 and His41) [30]. Meanwhile, the lowest bond energy will produce a molecule that has a constant temperature and pressure. The amino acid residues also influ- ence it in the binding domain of the target protein

and the type of chemical interactions that occur [32, 33].

Similar to another in-silico study about keam- pferol's potential to inhibit SARS-COV-2 M^Pro, Kaempferol 3-O-rutinoside as an active compound from Salvia officinalis, Artamesia dracunculus, and Zingiber officinale becomes a top three of 27 active compounds from an in silico analysis with best binding affinity −9.705 kcal/mol against M^Pro [34, 35]. Meanwhile in Zothantluanga et al., Kaempferol 3-O-α-L-rhamnopyranosyl-(1→4)-β- D-glucopyranoside as an active compound from Acacia pennata become a top three of 29 phyto compounds from an in-silico analysis with best binding affinity -7.2 kcal/mol to M^Pro using Auto- dock Vina on PyRx 0.8. However Kaempferol 3- O-α-L-rhamnopyranosyl-(1→4)-β-D-glucopyranoside was not selected for further studies due to bioavailability issues and low synthetic accessibil- ity [36]. Kaempferol was shown to have mutagenic potential in our research, indicating that its safety should be further examined.

Abietic acid is another chemical with a high average bond affinity. In silico study about Abietic acid against SARS-CoV-2 infection has not yet been established. However, an in-vitro study about SARS-CoV replication inhibition was performed Figure 1. Visualization of ACE2 receptor-ligand complex interactions with Ligands. (A) Abietic Acid (Yellow

stick) and (B) Kaempferol (Cyan stick)

(10)

by Ryu et al. The study explained that Abietic acid which was extracted from Torreya nucifera leaves was used as a positive control to inhibit SARS- CoV replication targeting 3CLpro which is also called SARS-CoV main protease (M^Pro). The inhibition rate was 58.0±4.8% at a concentration of 200 μM and the IC50 (The half maximal inhibitory concentration) value was 189.1±15.5 μM. How- ever Abietic acid inhibitor effect was not as good as other compounds [37]. The other study related to the antiviral potential of Abietic and Dehydro- abietic acid derivatives showed that these compounds were able to inhibit the activity of HHV-1 and HHV-2 (Human Herpes Simplex Virus type 1 and 2) compared to controls such as acyclovir and heparin. Abietic acid itself in this study had a mild antiviral effect on HHV-2 [38]. Data related to molecular docking between Abietic acid and M^Pro are still limited, so the interactions we found in our study show that hydrogen bonding interactions are found in the amino acids Leu141, His163, His173 and have a binding affinity of -7.5.

This study revealed the potential antiviral activity of Kaempferol and Abietic acid against the M^proand ACE-2 receptors. Regarding the good pharmacokinetic profile of Kaempferol and Abi- etic acid that fulfills the drug-likeness criteria by LR5, they can be listed as a candidate for oral SARS-CoV-2 M^pro inhibitor. Although further research with different designs is needed to confirm the exact mechanism of action for COVID-19 drug development.

Conclusion

The docking analysis ascertained Kaempferol and Abietic can impede the action of M^proand ACE-2 receptors. Kaempferol and Abietic have the same bond as the control and comply with the LR5 in possessing good pharmacokinetics. How- ever, Kaempferol has a predictable mutagenesis effect, while Abietic is rather safe. Abietic may have promising potential but further research is needed to determine the effectiveness of Abietic to treat COVID-19 using in-vitro and in-vivo studies.

Acknowledgement

The author would like to thank Alexander Patera Nugraha, DDS., MSc., PhD, for his support and discussion regarding this study.

References

1. García CAC, Sánchez EBA, Huerta DH, Gómez-Arnau J (2020) COVID-19 treatment-induced neuropsychiatric

adverse effects. Gen Hosp Psychiatry. doi:

10.1016/j.genhosppsych.2020.06.001.

2. Ralph R, Lew J, Zeng T et al. (2020) 2019-nCoV (Wu- han virus), a novel Coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness. The Journal of Infection in Developing Countries 14 (01): 3–

17. doi: 10.3855/jidc.12425.

3. Sohag AAM, Hannan MA, Rahman S et al. (2020) Re- visiting potential druggable targets against SARS-CoV- 2 and repurposing therapeutics under preclinical study and clinical trials: A comprehensive review. Drug Dev Res 1-23. doi: 10.1002/ddr.21709.

4. Bao L, Deng W, Huang B et al. (2020) The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature 583:

830–833. doi: 10.1038/s41586-020-2312-y.

5. Wan Y, Shang J, Graham R et al. (2020) Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. J Virol 94(7):e00127-20. doi:

10.1128/JVI.00127-20.

6. Wrapp D, Wang N, Corbett KS et al. (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, NY) 367 (6483): 1260–

1263. doi: 10.1126/science.abb2507.

7. Ferrario CM, Jessup J, Chappell MC et al. (2005) Effect of angiotensin-converting enzyme inhibition and angiotensin II receptor blockers on cardiac angiotensin-converting enzyme 2. Circulation. 111(20): 2605-10. doi:

10.1161/CIRCULATIONAHA.104.510461.

8. South AM, Brady TM, Flynn JT (2020) ACE2 (Angio- tensin-Converting Enzyme 2), COVID-19, and ACE In- hibitor and Ang II (Angiotensin II) Receptor Blocker Use During the Pandemic: The Pediatric Perspective.

Hypertension 76 (1): 16–22. doi: 10.1161/HYPERTEN- SIONAHA.120.15291.

9. Liu X, Wang XJ (2020) Potential inhibitors against 2019-nCoV coronavirus M protease from clinically ap- proved medicines. Journal of Genetics and Genomics 47 (2): 119–121. doi: 10.1016/j.jgg.2020.02.001.

10. Liu Y, Liang C, Xin L et al. (2020) The development of Coronavirus 3C-Like protease (3CLpro) inhibitors from 2010 to 2020. European Journal of Medicinal Chemistry 206: 112711. doi: 10.1016/j.ejmech.2020.112711.

11. Wu F, Zhao S, Yu B et al. (2020) A new coronavirus associated with human respiratory disease in China. Na- ture 579 (7798): 265–269. doi: 10.1038/s41586-020- 2008-3.

12. Hossain KS, Hossain MG, Moni A, Rahman MM, Rah- man UH, Alam M, Kundu S, Rahman MM, Hannan MA, Uddin MJ (2020) Prospects of honey in fighting against COVID-19: pharmacological insights and therapeutic promises. Heliyon 6(12): e05798. doi: 10.1016/j.heliyon.2020.e05798.

13. Kurniawan DB, Syaban MFR, Mufidah A et al. (2021) Protective effect of Saccharomyces cerevisiae in Rattus norvegicus Ischemic Stroke Model. Magister Thesis.

Universitas Brawijaya, Medical Education Department.

14. Pasupuleti VR, Sammugam L, Ramesh N, Gan SH (2017) Honey, Propolis, and Royal Jelly: A Comprehen- sive Review of Their Biological Actions and Health Ben- efits. Oxid Med Cell Longev 2017:1259510. doi:

10.1155/2017/1259510.

15. Osés SM, Marcos P, Azofra P et al. (2020) Phenolic Pro- file, Antioxidant Capacities and Enzymatic Inhibitory

(11)

JTLS | Journal of Tropical Life Science 229 Volume 12 | Number 2 | May | 2022 Activities of Propolis from Different Geographical Ar-

eas: Needs for Analytical Harmonization. Antioxidants 9(1): 75. doi: 10.3390/antiox9010075.

16. Elnakady YA, Rushdi AI, Franke R et al. (2017) Charac- teristics, chemical compositions and biological activities of propolis from Al-Bahah, Saudi Arabia. Sci Rep. doi:

10.1038/srep41453

17. Pobiega K, Gniewosz M, Krasniewska K (2017) Antimi- crobial and antiviral properties of different types of propolis. Zesz Probl Postępów Nauk Rol 589: 69–79. doi:

10.22630/ZPPNR.2017.589.22.

18. Kharisma V, Nugraha A (2020) Computational Study of Ginger (Zingiber Officinale) as E6 Inhibitor in Human Papillomavirus Type 16 (HPV-16) Infection. Biochemi- cal and Cellular Archives 20: 3155–3159. doi:

10.35124/bca.2020.20.S1.3155.

19. de Ruyck J, Brysbaert G, Blossey R, Lensink M (2016) Molecular docking as a popular tool in drug design, an in silico travel. Advances and Applications in Bioinfor- matics and Chemistry 9: 1–11. doi:

10.2147/AABC.S105289.

20. Joshi T, Joshi T, Sharma P et al. (2020) In silico screening of natural compounds against COVID-19 by targeting Mpro and ACE2 using molecular docking. European Review for Medical and Pharmacological Sciences 24 (8): 4529–4536. doi: 10.26355/eurrev_202004_21036.

21. Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small mol- ecules. Scientific Reports 7 (1): 42717. doi:

10.1038/srep42717.

22. Syaban MFR, Rachman HA, Arrahman AD et al. (2021) Allium Sativum As Antimalaria Agent Via Falciapin Protease-2 Inhibitor Mechanism : Molecular Docking Perspective. Clinical and Research Journal in Internal

Medicine 2 (1): 130–135. doi:

10.21776/ub.crjim.2021.002.01.4.

23. Pollastri MP (2010) Overview on the Rule of Five. Cur- rent Protocols in Pharmacology 49 (1): 9.12.1-9.12.8.

doi: doi: 10.1002/0471141755.ph0912s49.

24. Bohnert T, Prakash C (2012) ADME Proﬁling in Drug Discovery and Development: An Overview. Encyclope- dia of Drug Metabolism and Interactions. doi:

10.1002/9780470921920.edm021.

25. Chandrasekaran B, Abed SN, Al-Attraqchi O et al.

(2018) Computer-Aided Prediction of Pharmacokinetic (ADMET) Properties. In: Dos. Form Des. Parameters.

Elsevier. pp 731–755.

26. Syaban MFR, Erwan NE, Syamsuddin MRR et al. (2021) Molecular Docking Approach of Viscosin as Antibacte- rial for Methicillin-resistant Staphylococcus Aureus Via β-Lactamase Inhibitor Mechanism. Clinical and Re- search Journal in Internal Medicine 2 (2): 187–192. doi:

10.21776/ub.crjim.2021.002.02.4.

27. Susanto H, Kharisma VD, Listyorini D et al. (2018) Ef- fectivity of Black Tea Polyphenol in Adipogenesis Re- lated IGF-1 and Its Receptor Pathway Through In Silico

Based Study. Journal of Physics: Conference Series 1093 012037. doi: 10.1088/1742-6596/1093/1/012037.

28. Syaban M (2018) Analisis moleculer docking Beta glu- can sebagai terapi stroke iskemik pada target protein Brain Derived Neurotrophic Factor (BDNF). Magister Thesis. Universitas Brawijaya, Medical Education Department.

29. Toreti VC, Sato HH, Pastore GM, Park YK (2013) Re- cent Progress of Propolis for Its Biological and Chemical Compositions and Its Botanical Origin. Evidence-Based Complementary and Alternative Medicine 2013:

e697390. doi: 10.1155/2013/697390.

30. Harika MS, Kumar TR, Reddy LSS (2017) Docking Studies of Benzimidazole Derivatives using HEX 8.0.

International Journal of Pharmaceutical Sciences and Research 8(4): 1677-1688. doi: 10.13040/IJPSR.0975- 8232.

31. Rajalakshmi R, Lalitha P, Sharma SC et al. (2021) In sil- ico studies: Physicochemical properties, drug score, toxicity predictions and molecular docking of organosul- phur compounds against Diabetes mellitus. J Mol Recog- nit 34(11): e2925. doi: 10.1002/jmr.2925.

32. Nugraha RY, Faratisha IF, Mardhiyyah K et al. (2020) Antimalarial Properties of Isoquinoline Derivative from Streptomyces hygroscopicus subsp. Hygroscopicus: An In Silico Approach. BioMed Research International e6135696. doi: doi: 10.1155/2020/6135696.

33. Yueniwati Y, Syaban MFR, Erwan NE et al. (2021) Mo- lecular Docking Analysis of Ficus religiosa Active Com- pound with Anti-Inflammatory Activity by Targeting Tumour Necrosis Factor Alpha and Vascular Endothelial Growth Factor Receptor in Diabetic Wound Healing.

Open Access Macedonian Journal of Medical Sciences 9(A): 1031–1036. doi: 10.3889/oamjms.2021.7068.

34. Babaeekhou L, Ghane M, Abbas-Mohammadi M (2021) In silico targeting SARS-CoV-2 spike protein and main protease by biochemical compounds. Biologia 76 (11):

3547–3565. doi: 10.1007/s11756-021-00881-z.

35. Yueniwati Y, Syaban MFR, Faratisha IFD et al. (2021) Molecular Docking Approach of Natural Compound from Herbal Medicine in Java against Severe Acute Res- piratory Syndrome Coronavirus-2 Receptor. 9(A): 1181- 1186.doi: 10.3889/oamjms.2021.6963.

36. Zothantluanga JH, Gogoi N, Shakya A et al. (2021) Computational guided identification of potential leads from Acacia pennata (L.) Willd. as inhibitors for cellular entry and viral replication of SARS-CoV-2. Future Jour- nal of Pharmaceutical Sciences 7 (1): 201. doi:

10.1186/s43094-021-00348-7.

37. Ryu YB, Jeong HJ, Kim JH et al. (2010) Biflavonoids from Torreya nucifera displaying SARS-CoV 3CLpro inhibition. Bioorganic & Medicinal Chemistry 18 (22):

7940–7947. doi: 10.1016/j.bmc.2010.09.035.

38. García MPR (2014) Universitat Politècnica de València.

Ingeniería del Agua 18(1). doi: 10.4995/ia.2014.3293.

(12)

JTLS | Journal of Tropical Life Science 230 Volume 12 | Number 2 | May | 2022 This page is intentionally left blank.