Docking Study on Anti-HIV-1 Activity of Secondary Metabolites from Zingiberaceae Plants.

INTRODUCTION: Human immunodeficiency virus type-1 (HIV-1) that causes acquired immunodeficiency syndrome (AIDS) has become a worldwide health problem today. There are approximately 30 anti-HIV-1 drugs that have been used in the treatment of AIDS. However, effective anti HIV-1 agents with less side affect and high inhibition potency are still in demand.
OBJECTIVE: The objective of this study was to identify the potential compounds from Zingiberaceae plants that might be active as anti-HIV-1 by molecular docking.
MATERIALS AND METHODS: Molecular docking simulation was performed by using AutoDock 4.2 on Linux operation system. Docking protocol was validated by using root mean square deviation (RMSD) value using redocking and cross-docking methods. The reported metabolites from Zingiberaceae plants were docked on HIV-1 protease, integrase, and reverse transcriptase protein enzymes.
RESULTS: The docking result showed that the genera of Zingiber, Etlingera, Alpinia, Hedychium, and Boesenbergia have potential metabolites that inhibit HIV protease, integrase, and reverse transcriptase enzymes by possessing lower docking energy than native ligand of amprenavir, raltegravir, and nevirapine. Among the metabolites, noralpindenoside B and alpindenoside A from Alpinia densespicata inhibited protease enzymes with the lowest docking energy of -18.02 and -17.90 kcal/mol, respectively. Meanwhile, panduratin E from Boesenbergia pandurata Roxb. and 5α,8α-epidioxyergosta-6,22-dien-3β-ol from Etlingera elatior showed the lowest docking energy on integrase protein with docking energy of -11.97 and -11.41 kcal/mol, respectively. Pahangensin A from Alpinia pahangensis Ridley showed the lowest docking energy on reverse transcriptase enzyme with docking energy of -13.76 kcal/mol.
CONCLUSION: The docking molecular study has identified the possible potential compounds from Zingiberaceae plants that might be used for anti-HIV-1 treatment. So, this study suggested further isolation and purification of the predicted compounds. Copyright:

INTRODUCTION

Human immunodeficiency virus type-1 (HIV-1) is a kind of retrovirus family that causes acquired immunodeficiency syndrome (AIDS), which creates health crisis worldwide today. Many researchers have extensively studied for discovering new anti-HIV-1 agents. However, effective agents with less side effect and high inhibition potency are still in demand. Recently, approximately 30 anti-HIV-1 drugs have been licensed for the treatment of AIDS therapy. The mechanism of these drugs is by targeting the viral life cycle by inhibiting three important HIV-1 enzymes: HIV-1 protease (PR) that is essential for building the functional enzyme and support for viral maturation, HIV-1 integrase (IN) that integrates the transcribed double-stranded deoxyribonucleic acid (DNA) into the host chromosome, and HIV-1 reverse transcriptase (RT) that transcribes ribonucleic acid (RNA) to DNA viral.[113]

Docking is the computational application that can predict the interaction and binding energy of certain molecules on the specific target of protein receptors. It has been proven as an approach in drug discovery and development. Mostly, docking is used to identify one or more lead compounds that show higher affinity in receptor bindings. In natural product field, this method becomes an interesting tool to be used for virtually screening the complexity and diversity of natural compounds database for specific protein target that is responsible for a disease. For example, the discovery of potential anti-influenza compounds from Malaysian plant database NADI was done by using virtual screening method. Docking of the natural product library, targeting the dipeptidyl peptidase-4 (DPP-4) protein target was also reported.[45] Isolation of anticancer compound from Begonia sp based on the molecular docking approach was also reported.[668] Zingiberaceae, one of the most widely distributed plants in tropical and subtropical region, has 19 genus and 375 species distributed in Indonesia. Phytochemical and pharmacological properties of this plant were extensively studied by Indonesian researchers. On the basis of the data published in 2014, the family of Curcuma and Zingiber were the most studied plants with the percentage of 53.64% and 35.48%, respectively.[9] In Central Sulawesi, our previous study has identified 24 species of Zingiberaceae plants from Lore Lindu National Park (LLNP), which has been used traditionally by three different indigenous ethnics.[10]

The study of Zingiberaceae plants as anti-HIV-1 was conducted by some researchers. The chloroform extract of Boesenbergia pandurata rhizome and methanol extract of Alpinia galanga rhizome, showed potent inhibitory activity on HIV-1 PR. 5-Hydroxy-7-methoxyflavone and 5,7-dimethoxyflavone, isolated from Kaempferia parviflora, were reported to inhibit HIV-1 PR with half maximal inhibitory concentration (IC50) values of 19.04 and 19.54 μM, respectively. Zerumbone, the main compound from Zingiber zerumbet and Zingiber aromaticum, was reported to inhibit HIV with IC50 of 0.04 μg/mL.[111,12] 19S-19-acetoxychavicol acetate, isolated from A. galanga, was reported to block Rev transport that inhibits the replication of HIV type 1.[13] A new diarylheptanoid; (3S,5S)-3,5-diacetoxy-1,7-bis(3,4,5-trimethoxyphenyl) heptanes, 5αH-eudesmane-4α,11-diol, 5αH-eudesmane-4β,11-diol, 4α,10β-dihydroxy-1βH, 5αH-guaia-6-ene (guaianediol), and (+)-galanolactone from the rhizomes of Zingiber mekongense also showed anti-HIV activities.[14] Although, the study of Zingiberaceae on anti-HIV-1 activity has been performed well, the comprehensive study of Zingiberaceae metabolite compounds against three HIV protein enzymes (PR, IN, and RT) by using docking molecular approach is still not reported yet. Therefore, in this study, the secondary metabolites of Zingiberaceae plants from the complete genera—Alpinia, Curcuma, Etlingera, Hedychium, Boesenbergia, and Zingiber—were docked into the three HIV-1 protein enzymes; protease, integrase, and reverse transcriptase.

MATERIALS AND METHODS

Hardware and software

Docking molecular simulation was performed on Dell PC with Linux Fedora 3.6.11-4.fc16 i686 operating system, Intel® i5 CPU T5800 @ 2 GHz processor, and 4 GB of RAM. The software used for docking preparation was Chem3D Ultra 8.0, Ligprep, and AutoDock Tools (ADT) 1.4.5. Meanwhile, AutoDock 4.2.6 was used for running the docking simulation, and ADT 1.4.5 was used for analyzing the docking results.

Docking preparation

The secondary metabolites of Zingiberaceae plants were obtained from the KnapSack website (www.kanaya.naist.jp/knapsack_jsp/top.html) and literature.[914141617] There are 1070 chemical structures comprising 165 compounds from Zingiber, 79 compounds from Hedychium, 7 compounds from Etlingera, 91 compounds from Curcuma, 251 compounds from Boesenbergia (Kaempferia), and 477 compounds from Alpinia. The structures were modeled with Chem3D Ultra 8.0 (ACD labs) and optimized by Ligprep using OPLS_2005 force field. The optimized structure was assigned by using Epik at the target pH value of 7.0 ± 2.0. These conformations were used as starting conformations to perform docking. All HIV-1 protein enzyme structures were obtained from the X-ray crystal on Brookhaven Protein Data Bank (http://www.rcsb.org/pdb). Receptors were prepared for docking by AutoDock Tools (ADT). All heteroatom nonreceptor atoms in protein such as water and ions were removed. Kollman charges and solvation parameters were assigned to the protein atoms. Grid boxes, which comprised 40 × 40 × 40 points (x =16.751, y = 23.353, z = 17.611) spaced 0.375 Å apart, were used for PR enzymes; grid boxes, which comprised 28 × 42 × 28 points (x = -39.014, y = 31.127, z = -19.842) spaced 0.375 Å apart, were used for IN enzymes; and grid box, which comprised 50 × 50 × 50 points (x = 10.35, y = 14.076, z = 18.252) spaced 0.375 Å apart, was used for RT enzymes.

Docking calculation and validation

Docking of each ligand was run by AutoDock 4.2.6 with a Lamarckian genetic algorithm. The parameters were as follows: population size of 150, 250,000 energy evaluations, a mutation rate of 0.02, crossover rate of 0.80, and 100 independent docking runs. A cluster tolerance of 2.0 Å in positional root-mean square deviation (RMSD) was used to cluster the docking result. The ligand with the lowest free energy of binding was chosen as the best ligand conformation. Redocking and cross-docking experiments were used for validation of docking methods and parameter used. The redocking protocols are valid if the RMSD value is less than 2 Å.[6] The docking energy of ligands was then compared to native ligands.

RESULTS

The RMSD values obtained from cross-docking validation of HIV PR, HIV IN, and HIV RT are shown in Table 1. These RMSD values were from the best cluster conformations. Table 2 showed the top 10 docking results of the metabolite compounds from Zingiberaceae plants on HIV PR, IN, and RT enzymes.

Table 1

Root-mean square deviation value after redocking and cross-docking of three different ligands on HIV-1 protease, integrase, and reverse transcriptase enzymes

Protein target	PDB code	RMSD (Å)	Native ligand	Docking energy (kcal/mol)	Interaction with amino acids
HIV-1 protease	3NU3	1.403	Amprenavir	-14.61	ASP-25, ASP-125, GLY-127, ASP-129, ASP-130
HIV-1 integrase	3OYA	1.926	Raltegravir	-10.50	TYR-212, ASP-185, ASP-128, GLU-221
HIV-1 reverse transcriptase	3LP1	0.401	Nevirapine	-9.01	-

Table 2

Top 10 docking result of Zingiberaceae plants metabolite compounds on HIV-protease, integrase, and reverse transcriptase enzymes

No.	Metabolite compounds	Docking energy (kcal/ mol)	Interaction with amino acids	Plant source
HIV-1 protease enzyme
1	Noralpindenoside B	-18.02	ASP-130, ASP-129, ARG-8, GLY-148, VAL-82, THR-80, GLY-27, ASP-29, ARG-108	Alpinia densespicata
2	Alpindenoside A	-17.90	ARG-8, GLY-127, ASP-129, ASP-130, ASP-30, ASP-29, ARG-108	A. densespicata
3	Stigmasterol	-17.48	ASP-30	Hedychium coronarium
4	β-Sitosterol	-17.30	ASP-30	Zingiber officinale, Z. aromaticum
5	Panduratin G	-17.09	-	Boesenbergia pandurata Roxb.
6	Panduratin F	-17.07	ASP-25	B. pandurata Roxb.
7	Katsumadain A	-17.04	ASP-129, VAL-82, THR-80	Alpinia katsumadai
8	Blepharocalyxin D	-16.87	ARG-108, GLY-48, ASP-129	Alpinia blepharocalyx
9	Epicalyxin G	-16.87	ARG-108, ASP-130, ARG-8	A. blepharocalyx
10	Calyxin L	-16.86	ARG-108, GLY-127, ASP-30, ARG-8	A. blepharocalyx
HIV-1 Integrase enzyme
1	Panduratin E	-11.97	GLU-221, ASP-128, Mg2+	B. pandurata Roxb.
2	5α,8α-Epidioxyergosta-6,22- dien-3β-ol	-11.41	TYR-212, GLN-186	Etlingera elatior
3	Rubraine	-11.22	DA-17, Mg2+	A. katsumadai
4	Panduratin B1	-10.77	Mg2+	B. pandurata Roxb.
5	(-)- Krachaizin A	-10.75	TYR-212, ASP-185, Mg2+	B. pandurata Roxb.
6	Boesenbergin B	-10.74	GLU-221, ASP-128, Mg2+	B. pandurata Roxb.
7	Isorubraine	-10.69	DA-17, Mg2+	A. katsumadai
8	3-O-B-D-Glucopyranosil sitosterol	-10.65	-	Alpinia pinnanensis, A. blepharocalyx
9	Panduratin D	-10.57	Mg2+	B. pandurata Roxb.
10	(2S)-7,8-dihydro-5-hydroxy- 2-methyl-2-(4”-methyl- 3”-pentenyl)-8-phenyl- 2H,6H-benzo[1,2-b:5,4b’] dipyran-6-one	-10.56	DA-17, Mg2+	B. pandurata Roxb.
HIV-1 Reverse transcriptase enzyme
1	Pahangensin A	-13.76	LYS-101	A. pahangensis Ridley
2	(+)-Krachaizin A	-12.75	LYS-101	B. pandurata Roxb.
3	Shogasulfonic acid C	-11.76	LYS-101, LYS-104, HIS-235	Z. officinale
4	Isorubraine	-11.69	-	A. katsumadai
5	Panduratin B1	-11.43	-	B. pandurata Roxb.
6	Calyxin L	-11.42	GLN-91, LYS-101, ASN-103, HIS-235	A. blepharocalyx
7	(+)-Panduratin A	-11.41	-	B. pandurata Roxb.
8	(-)- Krachaizin A	-11.41	LYS-101	B. pandurata Roxb.
9	Blepharocalyxin D	-11.28	LYS-101, HIS-235, TYR-318	A. blepharocalyx
10	Boesenbergin A	-11.27	LYS-101	B. pandurata Roxb.

DISCUSSION

Current challenges on HIV-1 therapy have attracted many researchers to search for novel drugs from natural products. The available anti-HIV-1 drugs in the market now have limitations as they showed more side effects, poor drug–drug interactions, and were resistant against HIV-1. Although there are many studies regarding the HIV-1 inhibitory profiles of secondary metabolites from various plant species, it was reported that Zingiberaceae plants have less secondary metabolites for anti-HIV-1 activity compared to other plant species of different genera and family.[18] Therefore, the Zingiberaceae plant secondary metabolites have more opportunity to be further studied by applying the molecular docking to predict the potency of the metabolites on inhibiting the HIV-1 protein enzymes.

In this study, the docking simulation was performed on 1070 chemical compounds of Zingiberaceae plants on PR, IN, and RT protein enzymes using AutoDock 4.2.6.[19] The docking validation was based on RMSD value on cross-docking methods by redocking the native ligand of each receptors on three different targets. The crystal structure with the lowest RMSD value was selected for further study. PDB code 3NU3 for PR enzymes with amprenavir as native ligand, 3OYA for IN protein with raltegravir as native ligands, and 3LP1 for RT with nevirapine as native ligand was chosen with the lowest value of RMSD as 1.403, 1.926, and 0.401 Å, respectively. Meanwhile, the docking energy of native ligands of amprenavir, raltegravir, and nevirapine were -14.61, -10.50, and -9.01 kcal/mol, respectively [Table 1].

On the basis of docking results [Table 2], plants of Hedychium coronarium, Zingiber officinale, Z. aromaticum, B. pandurata Roxb., Alpinia katsumadai, and Alpinia blepharocalyx were the potential plants in which their metabolite compounds could inhibit the PR enzyme. Noralpindenoside B and alpindenoside A, a norditerpene and labdane glycosides from A. densespicata, were best docked on PR enzymes with docking energy of -18.02 and -17.9 kcal/mol, respectively, comparing native ligand amprenavir. These two compounds were reported to have NO inhibitory activity and no cytotoxic activity on four different cancer cell lines of HeLa, KB, Daoy, and WiDr.[20] Alpindenoside A was found to interact with ARG-8, GLY-127, ASP-129, ASP-130, ASP-30, ASP,-29, and ARG-108. Meanwhile, noralpindenoside B was found to interact with ASP-130, ASP-129, ARG-8, GLY-148, VAL-82, THR-80, GLY-27, ASP-29, and ARG-108.

Panduratin E, a cyclohexenyl chalcone from B. pandurata Roxb., and 5α,8α-epidioxyergosta-6,22-dien-3β-ol, a steroid compound from Etlingera elatior, were found to have the lowest docking energy on IN enzyme (-11.97 and -11.41 kcal/mol, respectively) and also better interaction than raltegravir. Panduratin E showed interaction with ASP-128, GLU-221, and Mg+2. Meanwhile, 5α,8α-epidioxyergosta-6,22-dien-3β-ol interacted with TYR-212 and GLN-186 on IN enzymes. The interaction of 5α,8α-epidioxyergosta-6,22-dien-3β-ol found between its epidioxy chain and TYR-212, as well as the π–π interaction between oxadiazole ring of raltegravir and TYR-212. E. elatior was reported to posses antioxidant, antifungal, antibacterial, cytotoxic, hepatoprotective, and anti-tyrosinase properties, and still no report on HIV-1 activity is available.[21] Beside these plants, A. katsumadai, Alpinia pinnanensis, and A. blepharocalyx, were also the potential plants that might have potential compounds for inhibiting the HIV-1 IN enzyme.

On HIV-RT enzyme, A. pahangensis Ridley, B. pandurata Roxb., Z. officinale, A. katsumadai, and A. blepharocalyx were plants that predicted to have potency in inhibiting HIV-1 RT enzyme. Pahangensin A, a diterpenoid isolated from A. pahangensis Ridley, showed best docked on RT enzyme with the docking energy of -13.76 kcal/mol and showed better interaction compared to nevirapine as well. It was found that the α,β-unsaturated γ-lactone ring possessed hydrogen bonding with LYS-101 at binding site of RT enzyme. Meanwhile, a part of labdanic diterpene inserted into the binding pocket of reverse transcriptase enzyme where nevirapine also interacted by hydrophobic interaction. This hydrogen bonding might contribute to the lowering score of docking energy of pahangensin A yielded for the more stable conformation than native ligand nevirapine. Pahangensin A was reported to possess antibacterial activity, and still no report on HIV-1 activity is available.[22]

CONCLUSION

Our docking study found that norditerpene and labdane glycosides, cyclohexenyl chalcone, steroid, and diterpenoids were the natural type compounds, predicted to possess inhibition activity on HIV-1 protein enzymes. Noralpindenoside B and alpindenoside A were suggested as inhibitors for HIV-1 PR enzyme, panduratin E and 5α,8α-epidioxyergosta-6,22-dien-3β-ol as HIV-1 IN enzyme inhibitors, and pahangensin A as HIV-RT protein enzyme inhibitor.

Financial support and sponsorship

Authors acknowledge the General Directorate of Research and Development, Ministry of Research and Technology, Republic of Indonesia for the funding financial support through Basic Research Grant with the contract number of 351.t/UN28.2/PL/2019.

Conflicts of interest

There are no conflicts of interest.