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Drug Designing: Open Access

Drug Designing: Open Access
Open Access

ISSN: 2169-0138

Research Article - (2021)Volume 10, Issue 1

Caribbean Plants as Source of Novel Inhibitors for Main Protease, NSP-15, and RNA-dependent RNA polymerase (RdRp) of SARS-Cov-2

Arya Duncan, Juchara Margetson, Jada Roberts, Taquanna Baron and Neelam Buxani*
 
*Correspondence: Neelam Buxani, Department of Chemical and Physical Sciences, College of Science and Mathematics, St. Thomas Campus, The University of the Virgin Islands, VI-00802, United States, Tel: +1(340)-693-1682, Email:

Author info »

Abstract

The Covid-19 pandemic with 74,299,042 confirmed cases including 1,669,982 deaths, reported worldwide by WHO (accessed 1:21 PM EST on 12/20/2020) is one of the most challenging situations the humankind is facing currently. Though some vaccines to treat this catastrophic disease have been developed on fast track, but still exploring the more potential alternative therapies is need of the hour. In search of new drug candidates to treat this pandemic, a structure based virtual screening study was carried out on the 125 compounds isolated from the native Caribbean medicinal plants like Aloe vera, Lemon grass, Moringa Olifera, and Lignum vitae, to determine their inhibitory potential against three main drug targets of SARS CoV-2; main protease (PDB ID: 6LZE), nsp 15 (PDB ID: 6WLC), and RNA-dependent RNA Polymerase (PDB ID: 7BV2) of SARS-CoV-2. The virtual screening workflow was performed using Schrodinger small molecule drug discover suite, in that compounds were prepared and docked in active sites of all three proteins. The co-crystallized ligand of every protein was used as a positive control and all docking scores were compared with it. Out of 125 compounds, 37 showed favorable docking interaction with the proteins compared to the native ligand. 13 compounds showed excellent docking score against 6LZE, out of that the most negative docking score (-11.962) was of rutin in compare to native ligand (-8.095), and it also showed more negative Prime MMGBSA binding energy-70.54 kcal/mol. In case of 7BV2, 35 compounds showed better docking results than the native ramdesivir (-4.566), docking score (-8.194) of vicenin-2 was best, it also exhibited almost same binding energy of complex (-44.54 Kcal/mol) as ramdesivir. In case of 6 WLC, in site 1, orientin showed most negative dockings core (-10.896), while in site 2 swertiajaponin’s docking score is-12.364. Pharmacokinetic (ADME) properties of 37 compounds were also calculated to ascertain the druglikeness of potential inhibitors. This study provides some lead molecules that might be helpful in designing drug for treating corona virus disease.

Keywords

Main protease; NSP-15: Nonstructural protein-15; RNA dependant RNA polymerase; Caribbean medicinal plants; Aloe vera; Lemon grass; Moringa Olifera; Lignum vitae

Introduction

The novel coronavirus SARS CoV-2, better known as COVID-19, is a new strain that belongs to the SARS family. This family of viruses replicates by binding to ACE receptors of cells and entering them to replicate. The virus itself consists of 2 subunits, one which binds to the ACE receptor and the other than binds to the cell surface to anchor the virus. The virus is most commonly found in a mass population among animals however, the new strain, SARS CoV-2 has been able to thrive among humans. A study of the genomic structure of the different coronavirus strains found that the new strain shares 88% similarity with the bat strain of SARS [1]. Reports state that the main mode of transmission for the SARS CoV-2 virus is through person-to-person contact specifically by way of droplets from an infected person coming into contact with a healthy host.

The trend of infection and symptom severity is directly linked to immune health whereby immunocompromised persons have a higher risk of infection and severe symptoms. Currently, 14 days is the known incubation period of the virus however there have been cases where the virus showed symptoms earlier or later than expected [2]. The main target of the virus is the respiratory system. As is common among the coronavirus family, symptoms presented include a dry coughing, fever, and fatigue however this new strain presented symptoms particular to the virus [3]. In addition to the aforementioned, SARS CoV-2 also caused disruption as the lower airway such as sneezing and sore throat in addition to gastrointestinal symptoms which are rare for the coronavirus family [3].

Due to how infectious the virus is, social distancing and mask regulations have been implemented leading to the shutdown or heavy patron restriction of closed spaces. Because of this disruption in day to day life, treatment for or immunity to the virus is necessary. Common methods of drug development take an extensive amount of time which is what makes computer-aided drug design a favorable computational tool. Computer-aided drug design is a computation drug design method that involves identifying active sites of target proteins and simulating protein- compound interactions to find inhibitors. The two types of computational drug design are structure-based drug design and ligand-based drug design [4]. Ligand-based drug design is used when the ligand structure is known but the receptor structure is unknown. Structure-based drug design on the other hand involves analyzing the known receptor structure to identify potential active sites, if unknown, and simulate ligand interactions at those sites to identify potential inhibitors that can compete with the biological ligand [4].

There are different proteins that are associated with SARS CoV- 2 functionality that are potential drug targets. Inhibition of these proteins could render the virus ineffective as interactions and mechanisms would be disrupted. The main protease (Mpro) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites [5]. The RNA dependent RNA polymerase (RdRp) has been evident to possess nsp (7,8,12); each RdRp acts as responsive cofactors when stimulating polymerase complex activities. The CoV nsp7/nsp8/nsp12 complex constitutes nucleotide polymerization for its configuration [6]. In addition, the nsp 15 (active hexamer) is responsible for providing structural attributes for the development of innovative therapeutic agents [7]. The SARS-CoV-2 polyprotein assists with transportation mechanisms functioning with maintenance, transcription, and replication of the virus genome.

In this study, four medicinal plants aloe vera, lemon grass, Moringa oleifera and Lignum vitae native to the Caribbean were chosen to determine the inhibitory effects of the antiviral compounds isolated from them on different SARS CoV-2 proteins. Based on the literature [8-11] a list of 125 compounds were compiled in Table 1 and were virtually docked in the active sites of Main protease, RNA dependent RNA Polymerase, and nsp-15 proteins of SARS- CoV-2 by using molecular docking program (GLIDE, Schrodinger). Docking scores and binding energies of protein-ligand complexes were compared with the native ligand of the chosen protein structures. ADME properties of selected compounds were also determined.

S. No. Compounds Plant Origin
1 Chrysophanol Aloe Vera
2 C-2'-decoumaroyl-aloeresin G Aloe Vera
3 Aloe emodin Aloe Vera
4 Aloe C-glucosylchromone Aloe Vera
5 Aloin Aloe Vera
6 4-methylpent-3-en-1-ol Aloe Vera
7 4,7-dihydroxy-5-methylcoumarin Aloe Vera
8 Aloe emodin anthrone Aloe Vera
9 Ruxolitinib phosphate Aloe Vera
10 Ruxolitinib Aloe Vera
11 Aloesin Aloe Vera
12 6-Methyl-1,3,8-trihydroxyanthraquinone (emodin) Aloe Vera
13 Luteolin-8-C-glucoside (orientin) Aloe Vera
14 Feruloylquinic acid Aloe Vera
15 10-Hydroxyaloin A Aloe Vera
16 Isovitexin Aloe Vera
17 Isoaloeresin D Aloe Vera
18 Aloin B Aloe Vera
19 5,3′-Dihydroxy-6,7,4′-trimethoxyflavone (eupatorin) Aloe Vera
20 Trihydroxy octadecenoic acid Aloe Vera
21 3,4-Di-O-caffeoylquinic acid Aloe Vera
22 6-methylhept-5-en-2-one Lemon Grass
23 Camphene Lemon Grass
24 Limonene Lemon Grass
25 Nonan-4-ol Lemon Grass
26 Citronellal Lemon Grass
27 Citronellol Lemon Grass
28 Neral Lemon Grass
29 Geraniol Lemon Grass
30 Citral Lemon Grass
31 Geranyl acetate Lemon Grass
32 β-caryophyllene Lemon Grass
33 γ-muurolene Lemon Grass
34 Caryophyllene oxide Lemon Grass
35 Swertiajaponin Lemon Grass
36 7-epi-ent-eudesmane-5,11-diol Lemon Grass
37 (2E,6E)-hedycaryol Lemon Grass
38 1,2-Benzenedicarboxylic acid,mono(2-ethylhexyl) ester Moringa Oleifera
39 1,3-dibenzyl urea Moringa Oleifera
40 2-Ethyl-2-propyl-1-hexanol Moringa Oleifera
41 3,3-dimethyloctane Moringa Oleifera
42 4- Dodecanol Moringa Oleifera
43 4-(-L-rhamnopyranosyloxy) benzyl glucosinolate (glucomoringin) Moringa Oleifera
44 4,6,8-Trimethyl-1-nonene Moringa Oleifera
45 All-E-lutein Moringa Oleifera
46 All-E-Zeaxanthin Moringa Oleifera
47 -Phellandrene Moringa Oleifera
48 Apigenin Moringa Oleifera
49 Arachidic acid Moringa Oleifera
50 Astragalin Moringa Oleifera
51 Aurantiamide acetate Moringa Oleifera
52 Behenic acid Moringa Oleifera
53 Benzyl glucosinolate (glucotropaeolin) Moringa Oleifera
54 Benzylamine Moringa Oleifera
55 β-sitosterol Moringa Oleifera
56 Caffeic acid Moringa Oleifera
57 Chlorogenic acid Moringa Oleifera
58 Cryptochlorogenic acid Moringa Oleifera
59 D-allose Moringa Oleifera
60 Dibutyl phthalate Moringa Oleifera
61 Ellagic acid Moringa Oleifera
62 Epicatechin Moringa Oleifera
63 Eugenol Moringa Oleifera
64 Ferulic acid Moringa Oleifera
65 Gallic acid Moringa Oleifera
66 Genistein Moringa Oleifera
67 Gentisic acid Moringa Oleifera
68 Glucoconringiin Moringa Oleifera
69 Glucoconringiin(1−) Moringa Oleifera
70 Hentriacontane Moringa Oleifera
71 Hexanedioic acid, bis (2-ethylhexyl) Moringa Oleifera
72 Isoquercetin Moringa Oleifera
73 Isorhamnetin Moringa Oleifera
74 Kaempferol Moringa Oleifera
75 Kaempferol-3-O--rhamnoside Moringa Oleifera
76 Kaempferol-3-O-glucoside Moringa Oleifera
77 Kaempferol-3-rutinoside Moringa Oleifera
78 Linoleic acid Moringa Oleifera
79 Linolenic acid Moringa Oleifera
80 Luteolin Moringa Oleifera
81 Marumoside A Moringa Oleifera
82 Marumoside B Moringa Oleifera
83 Moringyne Moringa Oleifera
84 Multiflorin B Moringa Oleifera
85 Myricetin Moringa Oleifera
86 Myristic acid Moringa Oleifera
87 N--L-rhamnopyranosyl vincosamide Moringa Oleifera
88 Niazimicin Moringa Oleifera
89 Niaziminin Moringa Oleifera
90 Niazirin Moringa Oleifera
91 Niazirinin Moringa Oleifera
92 o-Coumaric acid Moringa Oleifera
93 O-ethyl-4-[(-L-rhamnosyloxy)-benzyl] carbamate Moringa Oleifera
94 Oleic acid Moringa Oleifera
95 p-Coumaric acid Moringa Oleifera
96 p-Cymene Moringa Oleifera
97 Palmitoleic acid Moringa Oleifera
98 Procyanidin Moringa Oleifera
99 Pterygospermin Moringa Oleifera
100 Quercetin Moringa Oleifera
101 Rutin Moringa Oleifera
102 Salicylic acid Moringa Oleifera
103 Sinalbin Moringa Oleifera
104 Sinapic acid Moringa Oleifera
105 Squalene Moringa Oleifera
106 Stearic acid Moringa Oleifera
107 Syringic acid Moringa Oleifera
108 Tetracontane-1,40-diol Moringa Oleifera
109 Trimethyl (4-tert-butylphenoxy)silane Moringa Oleifera
110 Vanillin Moringa Oleifera
111 Vicenin-2 Moringa Oleifera
112 Z,Z-2,5-Pentadecadien-1-ol Moringa Oleifera
113 Ramonanin A Lignum Vitae
114 Ramonanin B Lignum Vitae
115 Ramonanin C Lignum Vitae
116 Ramonanin D Lignum Vitae
117 Gingerenone B Lignum Vitae
118 Glucoputranjivin(1−) Lignum Vitae
119 β-sesquiphellandrene Lignum Vitae
120 Glucoputranjivin Lignum Vitae
121 Pinocarveol Lignum Vitae
122 (2E,6E)-hedycaryol Lignum Vitae
123 Dodecane Lignum Vitae
124 Zingiberene Lignum Vitae
125 all-cis-octadeca-6,9,12,15-tetraenoic acid Lignum Vitae

Table 1: Complete list of compounds and their origin.

Materials and Methods

The virtual screening and molecular docking were performed using the Schrodinger small molecule drug discovery suite, Schrödinger Release 2020-2: Schrödinger, LLC, New York, NY, 2020.

Protein preparation and receptor grid generation

The COVID-19 proteins, main protease (PDB ID: 6LZE), RNA dependent RNA polymerase (PDB ID: 7BV2) and nsp-15 (PDB ID: 6WLC) were retrieved from the Protein Data Bank [12,13]. Using Schrodinger’s Protein Preparation Wizard the imported proteins were preprocessed, optimized, and minimized. During preprocessing of proteins missing hydrogens and residues were added with the help of Prime (version). As there was a bound ligand with all these proteins, so the receptor grids with the dimensions 10 Å × 10 Å × 10 Å were generated by selecting the atom of ligand molecule using Schrodinger receptor grid version 8.7.

Ligand preparation

A total of 4 medicinal plants native to the Caribbean were selected to compile a list of compounds to be virtually screened and identify potential antiviral agents for COVID-19. A literary analysis of numerous research papers and screening of databases generated compounds from each of the 4 plants for a total of 125 compounds (Table 1). The 2D chemical structures of all compounds discovered were imported from the PubChem database in SDF format into Maestro. Using Schrodinger’s LigPrep module, all the compounds were converted into 3D structures and optimized under Force field OPLS3e, different ionization states were generated at pH 7.0±2.0 using Epik module (version 5.2) Specific chiralities of 3D structures were retained, while around other chiral centers all possible stereoisomers were generated. Total 153 structures were taken to the docking analysis.

In present study, co-crystallized ligand of each protein was used as reference ligand; a peptide inhibitor {N}-[(2~{S})-3- cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})- 2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]- 1~{H}-indole-2-carboxamide (FHR) (Figure 1a) of main protease, Ramdesivir (Figure 1b) as an inhibitor of RdRp, and Uridine-5’- monophosphate (Figure 1c) inhibitor of nsp-15.

drug-designing-carboxamide

Figure 1a: {N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1- oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl] amino]propan-2-yl]-1~{H}-indole-2-carboxamide (FHR).

drug-designing-Ramdesivir

Figure 1b: Ramdesivir.

drug-designing-Uridine

Figure 1c: Uridine-5’-monophosphate.

Molecular docking

Using Glide Standard Precision (SP) the interaction between each protein and the 153 compounds and native ligand were analyzed. Based on the binding affinity scores generated (docking score), the compounds that had scores close to or better than the native ligand were selected for Extra Precision (XP) docking. Of the 153 docked compounds those with docking scores better than the native ligand for the protein were selected for further screening in XP mode along with the native ligand. If no compounds had a better docking score than the native ligand, compounds with glide scores-6.00 were chosen and further screened. The docking scores were again analyzed to determine which compounds, if any, have a higher affinity than the native ligand.

Further analysis of the compounds was necessary to determine the binding energy of protein-ligand complexes. With the knowledge of which compounds and poses best interacted with the protein, the compounds from XP mode were analyzed using Prime MM- GBSA. The SP and XP docking results showed that the various compounds interact with the protein and bind to the active site while Prime-MM-GBSA shows the free binding energy of the ligand-protein association.

ADME properties

The conclusion of the molecular docking study identified different compounds that interact well with the protein in comparison to the respective native ligand. Using QikProp (v6.4) of the Maestro (v12.4), the ADME properties of the top docking scorers were analyzed to determine if any of the compounds showed drug-like properties.

Results and Discussion

Structure-based virtual screening

Using the binding site of the native ligand, FHR, bound to the main protease 6LZE, a receptor grid of the active site was generated to dock the researched 125 compounds. An analysis of the active site showed the native ligand interaction via hydrogen bonds (H-Bond) with the GLY 143, PHE 140, HIE 163, and GLU 166 residues (Figures 2a-2c). Ligand preparation of the 125 researched compounds generated a total of 153 different poses to be filtered with all 153 meetings the filter parameters. Because of the small compound library, preliminary virtual screening was carried out in SP mode and a total of 38 compounds were filtered out based on their docking score. The SP mode docking results did not yield any compounds with a docking score better than the native (docking score=-9.734) so all compounds with scores equal to or greater than-6.00 were selected for XP virtual screening.

drug-designing-protein

Figure 2a: RInteraction diagram between 6LZE protein in complex with FHR.

drug-designing-complex

Figure 2b: Interaction diagram between 7BV2 protein in complex with Remdesivir.

drug-designing-site

Figure 2c: Interaction diagram between 6WLC protein in complex with Uridine-5'-Monophosphate (site 1 and 2 left to right).

Like the 6LZE protein, 7BV2 and 6WLC had their active site analyzed and the compounds docked to those sites in SP mode to determine top scorers. There were 40 compounds that had better docking scores than the native ligand when docked in SP mode to 7BV2. On the other hand, because 6WLC had 2 different sites, the compounds were docked in SP mode to both. Site 1 did not produce any compounds that had better docking scores than the native so all compounds with SP scores >6.00 were selected for XP docking. Site 2 on the other hand had 18 compounds with better docking scores than the native in SP mode. All compounds that scored better than the native or had an SP docking score >6.00 when no better interactions were produced were docked to their respective sites in XP mode.

The XP docking method was able to provide positive results as it showed there were compounds that interacted better than the native ligand. The XP docking yielded multiple compounds that had a better docking score than the native ligand for each protein (Tables 2-4).

Compounds XP docking score Molecular Weight Prime MMGBSA dG Bind (kcal/mol)
Rutin -11.962 610.524 -70.54
Vicenin-2 -10.001 594.525 -60.39
Procyanidins -9.747 594.528 -56.41
Kaempferol-3-Rutinoside -9.388 594.525 -47.29
Astragalin -9.369 448.382 -42.34
Kaempferol-3-O-Glucoside -9.369 448.382 -42.34
10-Hydroxyaloin A -9.217 434.399 -54.61
Marumoside B -9.031 459.449 -23.83
Multiflorin B -9.045 594.525 -22.96
Orientin -8.554 448.382 -54.66
Chlorogenic Acid -8.373 354.313 -18.06
Kaempferol-3-O--Rhamnoside -8.354 756.667 -40.47
Aloin -8.233 418.399 -52.31
FHR -8.095   -69.71

Table 2: Top scoring compounds from 6LZE docking.

Compounds XP docking score Molecular Weight Prime MMGBSA dG Bind (kcal/mol)
Vicenin-2 -8.194 594.525 -44.54
Multiflorin B -7.657 594.525 -29.57
Marumoside B -7.591 459.449 -38.5
3,4-Di-O-Caffeoylquinic Acid -7.585 516.457 -39.88
N-Alpha-L-Rhamnopyranosyl Vincosamide -7.468 660.674 -39.3
Isoquercetin -7.467 464.382 -32.69
Swertiajaponin -7.245 462.409 -29.12
Orientin -7.09 448.382 -48.84
Kaempferol-3-Rutinoside -7.008 594.525 -41.88
Aloin -6.912 418.399 -41.95
Glucotropeolin -6.561 409.425 -22.07
Chlorogenic Acid -6.412 354.313 -22.96
Astragalin -6.337 448.382 -32.72
Kaempferol-3-O-Glucoside -6.337 448.382 -32.72
D-Allose -6.184 180.157 -15.92
Sinalbin -6.18 425.425 -28.97
Niazimicin -6.147 357.421 -19.05
Isoaloeresin D -6.136 556.565 -42.16
Cryptochlorogenic Acid -6.017 354.313 -27.31
Glucoconringiin -6.004 391.408 -20.93
Glucoconringiin 1_ -6.004 391.408 -20.93
Glucoputranjivin -5.971 361.381 -22.8
Glucoputranjivin 1 -5.971 361.381 -22.79
Isovitexin -5.987 432.383 -30.58
10-Hydroxyaloin A -5.925 434.399 -30.2
Isorhamnetin -5.645 316.267 -9.1
Aloesin -5.617 394.377 -34.93
Kaempferol-3-O-Alpha-Rhamnoside -5.406 756.667 -37.95
Moringyne -5.286 312.319 -20.33
Niaziminin -4.984 399.458 -35.99
Niazirin -4.915 279.292 -32.1
Caffeic Acid -4.848 180.16 -22.94
Aloe Emodin Anthrone -4.815 256.257 -16.68
Gallic Acid -4.798 170.121 -18.32
O-Ethyl-4-[(Alpha-L-Rhamnosyloxy)-Benzyl] Carbamate -4.635 357.36 -29.36
Remdesivir (Native) -4.566   -44.66

Table 3: Top Scoring Compounds from 7BV2 docking.

  XP docking score Molecular Weight Prime MMGBSA dG Bind (kcal/mol)
Orientin S1 -10.896 448.382 -10.24
Uridine-5'-Monophosphate S1 -9.035   0
Swertiajaponin S2 -12.364 462.409 -10.24
Glucoconringiin S2 -11.691 391.408 0
Sinalbin S2 -11.543 425.425 0
Glucoconringiin 1- S2 -11.153 391.408 0
Aloesin S2 -10.411 394.377 -10.24
Uridine-5'-Monophosphate S2 -10.325   0
6WLC has 2 binding sites. The corresponding site for the compound is denoted as S1 (site 1) and S2 (site 2) -4.566 -4.566 -4.566

Table 4: Top scoring compounds from 6WLC docking.

The 6LZE protein had 13 compounds that docked better than the native ligand. These 13 interactions were analyzed using Prime MM-GBSA to determine the binding energy. Glide XP and Prime MM-GBSA scores for the top 13 compounds can be found in Table 2. The most prominent interaction between the protein- ligand complex was hydrogen bonding. In almost all complexes, hydrogen bonding occurred between the compound and the GLU 166 residue as is present in the native ligand-protein complex. This is the only common interaction when comparing the native ligand and the tested compounds, however when comparing the test compounds, hydrogen bonding with the CYS 145 residue and pi-pi stacking interaction between the HIE 41 residue and benzene derivatives are prominent (Figures 3a and 3b).

drug-designing-native

Figure 3a: 6LZE with FHR native ligand.

drug-designing-Rutin

Figure 3b: 6LZE with Rutin (top XP scorer).

The Prime MM-GBSA analysis showed the free binding energy of each compound-protein complex. The top 13 compounds had a range of free binding energy from-18.06 kcal/mol to-70.54 kcal/ mol. The complex with the lowest energy, which is most favorable, belongs to Rutin which also has better binding energy than the native ligand which would suggest a potentially strong inhibitor of the main protease. Rutin also had the best docking score at-11.962. The ligand interaction diagram shows H-Bonds with GLY 143 and GLU 166 residues the same as the native ligand but also interacts via hydrogen bonding with ASN 142, CYS 145, HIE 41, and GLN 189.

A total of 36 compounds had better ligand interactions than the native ligand of 7BV2. Similar to 6LZE, the main interactions between the protein and the ligands is hydrogen bonding. The native ligand interacts with the protein by hydrogen bonds with ASN 691, U10, POP 1003 and ring interactions with U 20 and ARG 555. The binding energy for the top compounds range from- 9.1 to-48.84. The compound Orientin has the most favorable Peime-MM GBSA binding energy (-48.84) and has a better docking score than the 7BV2 native ligand. The ligand interaction diagram for Orientin shows that its interaction with the protein is strictly via hydrogen bonding with A 11, U 12, A 13, A 12, A 14, C 15, ASN 496 (Figures 4a and 4b).

drug-designing-7BV2

Figure 4a: 7BV2 with Remdesivir native ligand.

drug-designing-Vicenin

Figure 4b: 7BV2 with Vicenin-2 (top XP scorer).

An analysis of the docking results for the 6WLC protein shows that one site has more favorable interactions with the compounds than the others. Only 1 of the 125 compounds interacts more favorably at site 1 (S1) than the native. Site 2 (S2) on the other hand had favorable interactions with 5 compounds (Table 4). The native ligand, Uridine-5'-Monophosphate, interacted with the protein via hydrogen bonding with LYS 65, ILE 64, SER 294 and LEU 346. Comparison of the native ligand interaction and the tested compounds shows that there are many residues in common between them. The tested compounds all form hydrogen bonds with at least one of the same residues as the native suggesting their importance in the active site and compound interactions (Figures 5a and 5d).

drug-designing-Uridine

Figure 5a: 6WLC with Uridine-5'-Monophosphate native ligand.

drug-designing-orienting

Figure 5b: 6WLC with orienting (top XP scorer S1).

In addition to the docking score, Prime MMGBSA analysis shows that these compounds have the most favorable binding energy out of all the protein-ligand interactions. The binding energy for the native ligand is 0 kcal/mol for both sites. Of the 6 total ligands that interacted with the protein irrespective of site, half have equal binding energy to the native and the other half have better binding energy than the native at-12.04 kcal/mol. The common residue interaction among all compounds aside from Aloesin is the SER 294 residue, suggesting it is a key residue in ligand interaction in the active site. A complete list of H-bonding interactions for the top scoring compounds is given in Tables 2-5.

Compounds Residues forming H-Bonding
Orientin SER 294, GLN 245, THR 341, HIS 250, HIS 235
Swertiajaponin SER 294, LYS 290, LYS 174, GLU 146, LEU 346, ASP 17
Glucoconringiin TYR 343, SER 294
Sinbalin SER 294, VAL 292
Glucoconringiin 1 GLU 146, LYS 174, SER 294, LYS 65
Aloesin HIS 235, GLN 245, GLU 146, LYS 65

Table 5: H-bonding interactions of Top Scoring Compounds with different residues of 6WLC.

Among all the compounds, one showed promising interaction with all three proteins. Orientin, a compound native to Aloe Vera, not only showed docking scores that were better than the native ligand for all proteins but also had a better binding affinity to the protein than the native. It showed higher affinity with the 7BV2 and 6WLC proteins and had a similar score for 6LZE. Prime MMGBSA and XP docking scores for Orientin and each protein’s native ligands can be found in their respective Tables 2-4 for 6LZE, 7BV2 and 6WLC respectively Table 6.

Compound Rule of 5 Donor HB Accept HB % Human oral absorption QPlogS QPlogPo/w QPlogKhsa #metab QPlogHERG QPPCaco QPlogBB
Rutin 3 9 20.55 0 -2.114 -2.536 -1.293 10 -5.217 1.158 -4.419
Vicenin-2 3 10 20.75 0 -3.016 -2.851 -1.333 15 -6.03 0.498 -5.182
Procyanidins 3 10 11.65 0 -3.622 0.082 -0.394 12 -5.892 1.024 -4.313
Kaempferol-3-rutinoside 3 8 19.8 0 -3.129 -1.944 -1.281 9 -6.392 1.458 -4.813
Astragalin 2 6 13 11.182 -2.741 -0.822 -0.79 7 -5.422 6.86 -3.27
Kaempferol-3-O-glucoside 2 6 13 11.182 -2.741 -0.822 -0.79 7 -5.422 6.86 -3.27
10-Hydroxyaloin A 1 6 12.45 22.877 -2.58 -0.895 -0.753 11 -4.86 6.16 -3.219
Marumoside B 2 8 18.55 0 -0.849 -3.009 -1.674 8 -3.63 4.509 -3.442
Multiflorin B 3 8 19.8 0 -2.513 -2.031 -1.225 9 -5.74 1.681 -4.334
Orientin 2 7 13 5.071 -2.752 -1.178 -0.747 10 -5.024 4.084 -3.343
Chlorogenic acid 1 6 9.65 17.723 -2.532 -0.239 -0.932 5 -3.304 1.936 -3.291
Kaempferol-3-O--rhamnoside 3 11 28.3 0 -2.411 -4.255 -2.13 12 -6.635 0.09 -7.139
Aloin 1 5 11.7 30.587 -2.657 -0.392 -0.623 11 -4.693 11.367 -2.803
3,4-Di-O-caffeoylquinic acid 3 7 11.45 1 -4.307 0.812 -0.628 6 -4.935 0.199 -5.305
N-alpha-L-rhamnopyranosyl vincosamide 3 7 23.9 1 -2.218 -1.998 -1.346 11 -6.917 1.673 -3.594
isoquercetin 2 7 13.75 1 -2.68 -1.394 -0.874 8 -5.379 2.192 -3.894
swertiajaponin 2 6 13 1 -3.292 -0.531 -0.696 10 -5.544 9.208 -3.205
Glucotropeolin 0 5 14 1 -1.37 -1.098 -1.339 6 -2.64 2.314 -3.061
D-allose 0 5 10.2 2 -1.045 -2.211 -0.873 4 -2.7 67.286 -1.569
Sinalbin 2 6 14.75 1 -1.404 -1.559 -1.396 7 -2.608 0.954 -3.515
niazimicin 0 4 9.55 3 -3.631 1.179 -0.483 4 -5.179 264.212 -1.521
Isoaloeresin D 2 5 14.5 1 -3.783 1.588 -0.342 10 -5.402 59.493 -2.531
Cryptochlorogenic acid 1 6 9.65 2 -2.115 -0.179 -0.913 5 -2.774 3.012 -2.857
glucoconringiin 2 6 14.75 1 -1.458 -1.837 -1.511 7 -2.598 1.314 -3.661
glucoconringiin 1- 2 6 14.75 1 -1.458 -1.837 -1.511 7 -2.598 1.314 -3.661
Glucoputranjivin 0 5 14 2 -1.392 -1.477 -1.412 6 -2.241 3.359 -2.961
Glucoputranjivin 1 0 5 14 2 -1.392 -1.477 -1.412 6 -2.241 3.359 -2.961
Isovitexin 1 6 12.25 2 -3.29 -0.591 -0.671 9 -5.688 8.105 -3.185
isorhamnetin 0 3 5.25 3 -3.458 1.232 -0.152 5 -5.169 59.672 -1.952
Aloesin 0 5 13.75 2 -2.747 -1.03 -0.884 9 -4.726 22.527 -2.648
Moringyne 0 4 10.5 3 -2.22 -0.087 -0.767 6 -4.43 212.456 -1.449
niaziminin 0 3 9.85 3 -5.202 2.314 -0.207 3 -5.984 387.686 -1.461
Niazirin 0 3 9.05 3 -3.062 -0.003 -0.75 4 -4.469 145.234 -1.608
Caffeic acid 0 3 3.5 2 -1.369 0.562 -0.792 2 -2.197 21.699 -1.576
Aloe emodin anthrone 0 1 3.2 3 -3.205 2.016 0.027 4 -4.568 224.785 -1.188
Gallic acid 0 4 4.25 2 -0.701 -0.567 -0.983 3 -1.417 10.04 -1.662
O-ethyl-4-[(alpha-L-rhamnosyloxy)-benzyl] carbamate 0 5 8.6 3 -3.142 0.681 -0.468 4 -4.952 65.672 -2.232

Table 6: ADME Properties.

ADME properties

The 13 best compounds from molecular docking went through ADME analysis using the QikProp module on Maestro. A total of 11 properties were the main focus which include the molecular weight, the number of hydrogen donors, the number of hydrogen acceptors, the number of violations of the rule of five, predicted IC50 value for blockage of HERG K+ channels (QPlogHERG), percent human oral absorption, predicted aqueous solubility (QPlogS), prediction of binding to human serum albumin (QPlogKhsa), predicted octanol/water partition coefficient (QPlogPo/w), predicted blood/brain partition coefficient (QPlogBB), number of likely metabolic reactions (#metab), and predicted apparent Caco-2 cell permeability (QPPCaco-).

ADME analysis showed that each compound has its pros and cons with no one compound falling within the acceptable range for all the properties. Most of the compounds had at least 1 violation of the rule of five with a few that had no violations. Lipinski Rule of Five states that drug-like compounds should have molecular weight lower than 500, lipophilicity (logP) lower than 5, less than five hydrogen bond donors, and less than 10 hydrogen bond acceptors, but many of natural products drugs do not comply with the “Rule of Five” [14]. it is recommended to not apply overly rigid cut-off points, as it increases the risk of losing some valuable compounds in earlier stages of screening [14], especially in case of natural products. A comprehensive list of the compounds and their ADME properties can be found in Table 6.

Conclusion

The researched plants are all used for medicinal purposes in the Caribbean from centuries. Based on the present in-silco study, multiple compounds showed promising inhibitory potential against different SARS CoV-2 proteins. Some of the compounds like rutin, vicenin-2, and Orientin exhibited better protein- compound association in compare to respective native ligands and found to have more negative binding energy. Further research on the antiviral properties of these plants against the various proteins of the SARS CoV-2 virus could prove useful for the discovery of naturally occurring antiviral compounds for future drugs and may provide natural remedies against this fatal disease.

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Author Info

Arya Duncan, Juchara Margetson, Jada Roberts, Taquanna Baron and Neelam Buxani*
 
Department of Chemical and Physical Sciences, College of Science and Mathematics, St. Thomas Campus, The University of the Virgin Islands, VI-00802, United States
 

Citation: Duncan A, Margetson J, Roberts J, Baron T, Buxani N (2021) Caribbean Plants as Source of Novel Inhibitors for Main Protease, NSP-15, and RNA-dependent RNA polymerase (RdRp) of SARS-Cov-2. Drug Des. 10:173.

Received: 21-Dec-2020 Accepted: 04-Jan-2021 Published: 11-Jan-2021 , DOI: 10.35248/2169-0138.21.10.173

Copyright: © 2021 Duncan A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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