









































  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

 
 

 
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. 

A SYSTEMATIC  
ANALYSIS OF  

COMPOUNDS PRESENT IN  
OCIMUM TENUIFLORUM 

(TULSI)  
REGARDING ITS  

ANTI-INFLAMMATORY 
PROPERTIES USING  

IN-SILICO TECHNIQUES   

JINAY PATEL, 
SONIA ARORA (FACULTY ADVISOR) 

 
 
 

✵ ABSTRACT 
The objective of this study was to gather 

data, create a database of the compounds present 
in Ocimum tenuiflorum (O. tenuiflorum), and gather 
related literature on the compounds found. A thor-
ough literature search was performed to gather in-
formation on compounds present in O. tenuiflorum, 
including chemical structures, relative abundance, 
presence in different plant parts, and availability 
from chemical supply vendors. The compounds’ 
chemical structures were refined using Discovery 
Studio Visualizer and Chimera software for future in-
silico docking studies. The structures with cleaned 
structural geometry were obtained through D.S. Vis-
ualizer for docking in the future. From the literature 
search of previously presented articles, it was found 
that methyl eugenol had the greatest percent com-
position in O. tenuiflorum. After searching the Pro-
tein Data Bank, COX-1, COX-2, and NF Kappa B 
were found to be the main protein targets of O. ten- 

uiflorum compounds in the arachidonic acid inflame 
matory pathway. Thus, the anti-inflammatory proper-
ties of O. tenuiflorum have been analyzed in this ar-
ticle for future in silico docking.       

 

1 INTRODUCTION 
Tulsi is a plant of the species Ocimum, scien-

tifically known as Ocimum tenuiflorum L. and more 
commonly known as “the holy basil.”[5] It is native to 
India and parts of North and Eastern Africa, China, 
Hainan Island, and Taiwan, where it is also titled as 
"the elixir of life" or "the queen of herbs."[5] Numer-
ous parts of O. tenuiflorum, such as the leaves, 
stems, and flower spikes, are traditionally used in 
Ayurveda and Siddha medicine for treating condi-
tions such as coughs, bronchitis, fever, and bile dis-
turbances.[5] Ayurveda and Siddha medicines are 
two of the most ancient medicinal branches of India 
based on herbal and mineral compounds. O. tenui-
florum has also been vividly known for its anti-inflam-
matory, antiseptic, and other numerous organ pro-
tective properties.[5] Based on its prominent medici-
nal uses, the Ocimum tenuiflorum was chosen for fur-
ther investigation. In this study, the focus was on in-
flammation because it is a well-known symptom of 
numerous infectious and non-infectious diseases. 
Various in vitro and in vivo studies have documented 
the anti-inflammatory effects of O. tenuiflorum, and 
it has been suggested that O. tenuiflorum has many 
bioactive secondary metabolites that help inhibit 
certain inflammatory pathways synergistically or 
alone.[6]  

Arachidonic acid is the major polyunsatu-
rated fatty acid present in mammalian systems, 
which is oxygenated by three important pathways— 
the cyclooxygenase (COX), the lipoxygenase (LOX), 
and the epoxygenase pathways.[10] The inhibition of 
COX and LOX pathways in arachidonic acid metab-
olism in conjunction with major O. tenuiflorum com-
pounds like eugenol and linoleic acid contributes to 
the anti-inflammatory action of O. tenuiflorum, ob-
served in both acute and chronic inflammatory mod-
els in animals.[4] This observation suggests that cer-
tain compounds present within O. tenuiflorum are 
responsible for anti-inflammatory responses in ani- 



  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

mal models. This implication can be further explored 
to determine which compounds in O. tenuiflorum 
may induce anti-inflammatory activity in humans. As 
a result, O. tenuiflorum has demonstrated anti-in-
flammatory effects normally observed in nonsteroi-
dal anti-inflammatory drugs (NSAID) such as phenyl-
butazone, ibuprofen, naproxen, aspirin, and indo-
methacin.[4] The inhibition of the cyclooxygenase en-
zymes COX-1 and COX-2 is what drives the NSAID 
mechanism.[1] Although NSAIDS are effective, they 
have a few common side effects, such as nausea, 
dyspepsia, vomiting, and skin reactions. On the con-
trary, herbal medications are devoid of such side ef-
fects, which illustrates the importance of conducting 
a study of the compounds found in O. tenuiflorum: 
it may open the path for herbal NSAIDs without 
these side effects.[1]  

O. tenuiflorum has various transcription fac-
tors, one of which is the nuclear factor-Kappa B (NF 
Kappa B). NF Kappa B is one of the major regulators 
of inflammation, cellular transformation, tumor cell 
survival, proliferation, invasion, angiogenesis, and 
metastasis as compared to the other transcription 
factors.[11] Plants of the Ocimum species are known 
to have an abundance of terpenes.[7] Additionally, 
plant isolates containing terpenoids (a modified 
class of terpenes) have been found to suppress NF 
kappa B signaling, a protein complex linked to the 
pathogenesis of inflammatory diseases, cancer, viral 
infection, and autoimmune diseases.[7] Thus, the 
study of O. tenuiflorum for anti-inflammatory proper-
ties is vital. There are numerous compounds present 
in the Ocimum species amongst which methyl euge-
nol, β-selinene, γ-murolene, rosmarinic acid (phe-
nolic), ursolic acid, and camphene are some major 
ones based on their percentage of makeup. These 
and other compounds from O. tenuiflorum have 
been characterized and analyzed in this study to 
form an extensive database. This database is used to 
determine which of the compounds identified would 
interact with desirable molecular targets and de-
crease inflammation in future studies. 

Therefore, in this study, an in-silico approach 
was used to refine the compounds present in O. ten-
uiflorum and to develop a highly detailed database 
to be used for future purposes, such as investigating 

how an individual compound from O. tenuiflorum 
extract will interact with these molecular targets. This 
interaction would be detailed using the in-silico 
docking mechanism, which is a molecular model-
ing technique that is used to predict how a protein 
(enzyme) interacts with small molecules (ligands) to 
deduce their mechanism of action on targets found 
in future dry labs.  

 

2 METHODOLOGY  

First, a literature search was conducted 
through Pubchem to create a list of well-known com-
pounds present in O. tenuiflorum and their percent 
composition in the part of the plant they are found 
in.[8] The vendors that distribute the compound in 
the USA were identified from PubChem as well  
(TABLE 1).[8] Next, the collection of the virtual structures 
of all the compounds was created and the files were 
saved in the SDS (2D) formats (FIGURE 1). Then, within 
the structural data, the pharmacology and biochem-
istry of the compounds were reviewed for each com-
pound from PubChem in order to get an idea of the 
mechanism of action and the aspects of human in-
teraction associated with the individual com-
pounds.[8] This was an adaptation process, so new 
compounds were added to the list when and if they 
were discovered throughout the study.  

Later, software such as Discovery Studio 
(D.S.) Visualizer (BIOVIA Dasasult Systemes, San Di-
ego, CA, USA) and Chimera were downloaded.[9] 
Chimera was used to convert the mol format files 
into sybyl mol 2 format files for compatibility within 
D.S. Visualizer. The sybyl mol 2 format files were then 
opened in D.S. visualizer, wherein hydrogen atoms 
were added to the structure. The geometry of the hy-
drogen atoms was cleaned and 3D coordinates were 
assigned to them. The three-dimensional structure 
was then saved as sybyl mol 2 format files (FIGURE 2). 
The formats sybyl mol 2 and SDS were employed to 
have a better approximation of the structure of the 
compounds, and to notice the 2D and 3D differ-
ences in the molecules, which would visually assist in 
the molecular docking. 

And finally, another literary search was con-
ducted on the Protein Data Bank for the inflamma-
tory molecular pathways and O. tenuiflorum within  



  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

   

 COMPOUNDS PERCENTAGE FOUND VENDORS PART OF PLANT 
     

1.  1,8-CINEOLE TRACE(T) ALL  LEAVES 

2.  1,10 DI-EPI-CUBENOL 1.8 N/A LEAVES 

3.  3,4-DIMETHOXYCINNAMIC ACID (PHENOLIC) N/A ALL  N/A 

4.  3.4.5-TRIMETHOXYCINNAMIC ACID N/A 1,2,4 N/A 

5.  4.4′-METHYLENE-BIS (2-METHYL ANILINE) N/A N/A N/A 

6.  Α-ELEMENE   0.5 2 FLOWER SPIKES 

7.  Α-HUMULENE   0.2 4 LEAVES 

8.  Α-PINENE 0.2 2 LEAVES 

9.  Α-TERPINEOL   TRACE(T) 1,2,3 LEAVES 

10.  ALLOAROMADENDRENE 1.16 N/A N/A 

11.  APIGENIN N/A 2 LEAVES 

12.  Β-BOURBONENE   0.2 N/A LEAVES 

13.  Β-CUBEBENE   0.1 2,4 FLOWER SPIKES 

14.  Β-PINENE   0.1 2,3  LEAVES 

15.  Β-SELINENE 3.3 2,4 LEAVES 

16.  Β- SESQUIPHELLANDRENE 0.2 N/A LEAVES, FLOWER SPIKES 

17.  BAICALIN (LAVONOIDS) N/A 2,4 N/A 

18.  BENZALDEHYDE 0.44 2,4 LEAVES 

19.  BICYCLOGERMACRENE TRACE(T) N/A LEAVES 

20.  CAFFEIC ACID (PHENOLIC) N/A ALL  LEAVES 

21.  CAMPHENE   0.1 1,2,3 LEAVES 

22.  CAMPHOR    0.1 2,3 LEAVES 

23.  CARNOSIC ACID N/A 2,4 N/A 

24.  CHRYSOERIOL (FLAVON) N/A 1,2,4 N/A 

25.  CI Α-COPAENE   1.9 N/A LEAVES, FLOWER SPIKES 

26.  CI Α-CUBEBENE   TRACE(T) 4 FLOWER SPIKES 

27.  CI Β-CARYOPHYLLENE   4.1 2,3,4 LEAVES 

28.  CI Β-GURJUNENE   TRACE(T) N/A LEAVES 

29.  CI BORNEOL    2.4 2 LEAVES 

30.  CI TERPIN-4-OL   0.1 2,3 LEAVES, STEM 

31.  CUBEBOL   0.3 N/A LEAVES 

32.  DI (ETHYLHEXYL) PHTHALATE N/A 1,2 N/A 

33.  DI-N-BUTYL PHTHALATE, DIBUTYL PHTHALATE N/A 1,2,4 LEAVES 
     

TABLE 1: This table shows various compounds found in specific parts of O. tenuiflorum such as the leaves, stem, or flower spikes. 
It also includes their percentage composition, the vendors who supply them in the USA, and their PubChem SID and Purchas-
able Chemical ID. Some of the compounds have trace(t) in their “Percentage Found” column, which implies that the compound 
is present in a quantity too small to be measured. PubChem[8]  
 



  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

   

 COMPOUNDS PERCENTAGE FOUND VENDORS PART OF PLANT 
     

34.  DIOSMETIN (FLAVONE GLYCOSIDE) N/A 1,2,4 N/A 

35.  (E)-Α-BERGAMOTENE 0.72 2,4 LEAVES, FLOWER SPIKES 

36.  (E)-Β-OCIMENE 1.9 2,4 LEAVES 

37.  E-METHYL CINNAMATE 1.5 ALL  LEAVES, STEM 

38.  EPI-Α-CADINOL 1.03 N/A LEAVES 

39.  ESTRAGOL N/A 1,2,4 LEAVES, FLOWER SPIKES 

40.  EUGENOL   0.9 ALL  LEAVES 

41.  Γ-MUROLENE 5.82 2 LEAVES 

42.  GERMACRENE A   0.7 N/A LEAVES 

43.  GERMACRENE D   2.3 2,4 LEAVES 

44.  GERANIOL TRACE(T) ALL  LEAVES 

45.  GLOBULOL 1.05 2,4 N/A 

46.  ISOSAKURANETIN (LAVANONE) N/A 4 N/A 

47.  KAEMPFEROL N/A ALL  N/A 

48.  LINALOOL    0.5 3 LEAVES 

49.  LIMONENE   0.2 1,2 LEAVES 

50.  LUTEOLIN (FLAVONOID) 0.5 N/A LEAVES 

51.  METHYL CHAVICOL   TRACE(T) 1,2,3 LEAVES 

52.  METHYL EUGENOL   82.9 2,3,4 LEAVES 

53.  MYRTENAL N/A 2 LEAVES 

54.  NEVADENSIN (FLAVONES, GLYCOSIDES) N/A 2,4 N/A 

55.  P-CYMENE   TRACE(T) 1,2,3 FLOWER SPIKES 

56.  PEDUNCULIN N/A N/A N/A 

57.  PERMETHRIN N/A 1,2 N/A 

58.  PEINIDIN (ANTHOCYANIDINS) N/A N/A N/A 

59.  ROSMARINIC ACID (PHENOLIC) 0.27 2,4 LEAVES, STEMS 

60.  SABINENE   TRACE(T) 2 LEAVES 

61.  Δ-CADINENE   1.1 2,4 LEAVES 

62.  (TRANS)-Β-FARNESENE 0.12 2,4 LEAVES 

63.  (TRANS)-Β-GUAIENE 0.29 N/A LEAVES 

64.  URSOLIC ACID 2.5 1,2,4 LEAVES 

65.  XANTHOMICROL N/A 2 STEM 

66.  (Z)-3-HEXANOL 1.8 1,2 LEAVES 
     

 

VENDORS 
1) TIM TEC 
2) MUSECHEM 
3) ACROS ORGANICS 
4) ZINC 

   

     

TABLE 1 CONTINUED 



  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

the context of inflammation and its molecular targets 
concerning humans.[2] This search was conducted to 
determine which molecular target should be further 
used to analyze the docking compatibilities of the 
compiled O. tenuiflorum compounds.  

3 RESULTS 
A detailed database was created in TABLE 1 to 

compile an extensive list of 66 compounds in O. ten-
uiflorum. TABLE 1 also displays information about the 
percentage of a particular compound present in cer-
tain parts of O. tenuiflorum, such as the leaves, stem, 
flower spikes, etc. In TABLE 1, it is evident that most of 
the compounds were available from the list of US-
based vendors like Tim Tec, Musechem, Acros or-
ganics, and ZINC. The PubChem SID and Purchasa-
ble Chemical ID were also available for all of the 
compounds. The highest percentage of composi-
tion for a compound in O. tenuiflorum was for methyl 
eugenol, about 82.9% within the leaves, which was 
available from Musechem, Acros organics, and ZINC 
(TABLE 1). Overall, a total of 66 compounds were iden-
tified to be present in O. tenuiflorum. Out of those 
compounds, many were in trace amounts and some 
did not have any data on the percentage of their 
presence (TABLE 1). 

Next, 2D structures in SDS format files were 
obtained from PubChem in the form of 2D 
ChemDraw files (FIGURE 1). FIGURE 1 shows the chemical 
structure of a few major compounds found in O. ten-
uiflorum. The compounds seen were not ready for 
docking since they had not been refined yet to allow 
for further in-silico processes due to their structural 
ambiguity. It would be difficult to dock them; there-
fore, further work on each compound was needed, 
such as adding hydrogens and removing unwanted 
ions (FIGURE 1). Next, the refined structures were ob-
tained from D.S. Visualizer in order to transfer the co-
ordinates to proceed to the in-silico docking step 
(FIGURE 2). The refined structure of several O. tenuiflo-
rum compounds are portrayed in FIGURE 2. 

Finally, the literature search on the Protein 
Data Bank yielded that COX-1, COX-2, and NF 
Kappa B were the anti-inflammatory target proteins 
that interact with certain compounds found in O. ten-
uiflorum. However, within the Protein Data Bank the 
COX-2 protein was the most prevalent target found 
in humans and COX-1 had the least human entries. 
These targets will be explored in future studies with 
the collected O. tenuiflorum database compounds. 
  

 

FIGURE 1: The 2D structures of compounds present in  
O. tenuiflorum are shown here, such as ursolic acid, methyl 
eugenol, γ-murolene, rosmarinic acid, camphene, and  
β-selinene. Some of the figures that were downloaded 
from PubChem portray the oxygen and hydroxide atoms 
in red fonts. 

 

FIGURE 2: 3D structures of a few of the major compounds 
present in O. tenuiflorum, such as camphene, methyl eu-
genol, rosmarinic acid, β-selinene and γ-murolene with hy-
drogen atoms added and their geometry cleaned. 



  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

4 DISCUSSION & CONCLUSION 
For this study, a thorough database was cre-

ated for various compounds present in different 
parts of O. tenuiflorum. This database is being 
stored on the computers in the Arora lab to be used 
for future studies. During the literary search of these 
structures, it was found that methyl eugenol was the 
most abundant compound and γ-Murolene was the 
second most abundant compound. Both com-
pounds are present in the leaves of O. tenuiflorum. 
These compounds are significant because they are 
present in such high abundance, which suggests 
that they might have an important role in the anti-in-
flammatory effect of O. tenuiflorum. To test this state-
ment, these structures will have to be run through in-
silico docking modules to determine whether the 
abundance has any correlation with the anti-inflam-
matory effect.  

Moreover, the purpose of attaining the 2D 
files was to make the structures available before re-
finement so that they could be reviewed when re-
quired. The refined structures with cleaned geome-
try were obtained so that their docking sites were 
clear of any hindrance and to ensure that docking 
could be done properly in the future. Also, the target 
proteins were identified from the Protein Data Bank 
so that they could be used along with their ligands 
to dock. Thus, the future goal is to use in-silico ap-
proaches to discover how compounds will interact 
with various molecular targets and inflammatory 
pathways, specifically COX-2, as it is the most preva-
lent target yielded in most searches related to hu-
man query within the Protein Data Bank. The data-
base gathered in this study will be crucial for future 
studies to identify which compounds present in O. 
tenuiflorum are attributed to its anti-inflammatory 
properties. This information could in turn allow for 
the development of herbal anti-inflammatory medi-
cation with minimal side effects∎  
 

5 ACKNOWLEDGEMENTS 
I would like to thank my mentor and supervi-

sor Dr. Sonia Arora for her invaluable support and 
knowledge behind this paper and research. Her pas-
sion for the subject, along with attention to detail has 
been greatly inspiring, allowing me to diligently 

work on this research project. Her ingenious remarks 
and constructive criticism for various drafts of this pa-
per has allowed for this research paper to be suc-
cessfully completed. I will always be extremely grate-
ful to Dr. Arora for imparting me with the knowledge 
and wisdom about in-silico approaches, which can 
be used to create comprehensive databases in any 
research work. 

 

6 REFERENCES  
[1] Ahmad A., Abuzinadah M.F., Alkreathy H.M., Banaganapalli 

B., & Mujeeb M. (2018). Ursolic acid rich Ocimum sanctum L 
leaf extract loaded nanostructured lipid carriers ameliorate 
adjuvant induced arthritis in rats by inhibition of COX-1, 
COX-2, TNF-α and IL-1: Pharmacological and docking stud-
ies. PLoS ONE, 13(3), E0193451.  

[2]  Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. 
N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2020). The 
Protein Data Bank. Nucleic acids research, 28(1), 235–242. 

[3]  Biovia, Dassault Systemes, Discovery Studio Visualizer, Ver-
sion 20.1, San Diego: Dassault Systèmes, (2020). 

[4]  Cohen M. M. (2014). Tulsi—Ocimum sanctum: A herb for all 
reasons. Journal of Ayurveda and integrative medicine, 5(4), 
251–259.  

[5]  Flegkas A., Milosević Ifantis T., Barda C., Samara P., Tsitsilonis 
O., & Skaltsa H. (2019). Antiproliferative Activity of (-)-
Rabdosiin Isolated from Ocimum sanctum L.  Medicines, 
6(1), 37.  

[6]  Jamshidi, N., & Cohen, M. M. (2017). The Clinical Efficacy 
and Safety of Tulsi in Humans: A Systematic Review of the 
Literature. Evidence-based complementary and alternative 
medicine. Evidence-based Complimentary and Alternative 
Medicine: eCAM, 2017, 9217567. 

[7]  Kapewangolo, P., Omolo, J. J., Bruwer, R., Fonteh, P., & 
Meyer, D. (2015). Antioxidant and anti-inflammatory activity 
of Ocimum labiatum extract and isolated labdane diterpe-
noid. Journal of inflammation (London, England), 12, 4. 

[8]  Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, 
Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., 
Zhang, J., & Bolton, E. E. (2019). PubChem 2019 update: Im-
proved access to chemical data. Nucleic acids research, 
47(D1), D1102–D1109.  

[9] Pettersen EF, Goddard TD, Huang CC, Couch GS, Green-
blatt DM, Meng EC, Ferrin TE. (2004). UCSF Chimera—A vis-
ualization system for exploratory research and analysis.  
J Comput Chem. 25(13):1605-1612. 

[10] Reddy, K. K., Vidya Rajan, V. K., Gupta, A., Aparoy, P., & Red-
danna, P. (2015). Exploration of binding site pattern in ara-
chidonic acid metabolizing enzymes, Cyclooxygenases and 
Lipoxygenases. BMC research notes, 8, 152. 

[11] Yadav, V. R., Prasad, S., Sung, B., Kannappan, R., & Aggarwal, 
B. B. (2010). Targeting inflammatory pathways by triterpe-
noids for prevention and treatment of cancer. Toxins, 2(10), 
2428–2466. 



  ARESTY  RUTGERS UNDERGRADUATE RESEARCH JOURNAL, VOLUME I, ISSUE III 
 
 
 

 

Jinay Patel is Rutgers University graduate, having B.S degree in Biotechnology and Plant Science 
from School of Environmental and Biological Science. His research was on O. tenuiflorum to gather 
the data on the compounds present within it and study its anti-inflammatory properties using In-
Silico techniques. He is currently working as a QC analyst at Roche Molecular Systems within enzy-
matic department and in the future, he would like to attend graduate school and study drug devel-
opment. Education in drug development for him would entail discovering new medicines and 
treating diseases to support better patient care. The following research on O. tenuiflorum is one of 
the crucial steps for him in attaining this goal. 

 


