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POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2

NON STRUCTURAL PROTEINS (NSP9/NSP10)

RAMIL S. LUCAS

An Undergraduate Research Presented to:

The Faculty of the Chemistry and Environmental Science

College of Arts and Sciences

NUEVA ECIJA UNIVERSITY OF SCIENCE AND TECHNOLOGY

Cabanatuan City, Philippines

In Partial Fulfillment of

Requirements for the Degree of

BACHELOR OF SCIENCE IN CHEMISTRY

MAY 2022

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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APPROVAL SHEET

The thesis entitled: POTENTIAL ANTIVIRAL PROPERTIES OF

BIOACTIVE COMPOUNDS AND PHYTOCHEMICALS FROM SELECTED

PLANTS AGAINST SARS-COV-2 NON STRUCTURAL PROTEINS

(NSP9/NSP10) prepared and submitted by RAMIL S. LUCAS in partial fulfillment of the

requirements for the degree of BACHELOR OF SCIENCE IN CHEMISTRY is hereby

endorsed:

DANILET VI M. MENDOZA, RCh. DARWIN F. REYES, RCh.

Adviser Critic

Date Date

JUNE ALEXIS A. SANTOS, RCh. MARILENE C. HIPOLITO, RCh.

Co-adviser Research Professor
____________
Date Date

Accepted and approved in partial fulfillment of the requirements for the degree of

Bachelor of Science Chemistry

DARWIN F. REYES, RCh. EnP. JAN RAMEL A. TUMBAGA, PhD.

Department Chair Research, Extension and Training Chair

Date Date

MARIO M. ABESAMIS Jr., RCh, PhD.

College Dean

Date

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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BIOGRAPHICAL DATA

The author, Ramil Sebastian Lucas, was born on April 19, 2000 in Talavera, Nueva

Ecija. Ramil is currently taking Bachelor in Science in Chemistry at the Nueva Ecija

University of Science and Technology. He is the second son of Mr. and Mrs. Lucas.

Ramil spent his primary education, at the Talavera Central School, and took his

secondary education at the Talavera National High School. Ramil graduated with honors

under the Science, Technology, Engineering, and Mathematics strand in senior high school

at the same school. During his fresh years, Ramil became a sports committee in the College

of Arts and Sciences Student Council. Ramil also became the Vice President of the

Chemical Society of the Philippines-NEUST Chapter when he was in his second year on

the program.

RAMIL SEBASTIAN LUCAS

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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ACKNOWLEDGEMENTS

Boundless gratitude and appreciation for the help from the following persons who

contributed to make this study within reach.

Mrs. Danilet Vi M. Mendoza, RCh., MSc., the research adviser. The researcher’s

deepest gratitude for her because of her suggestions, comments, recommendations,

checking of every chapter, guidance, and support to make this study doable.

Mr. June Alexis A. Santos, RCh., the previous adviser of the researcher who

taught the researcher the wonders of computational type of research. Immeasurable

appreciation for the efforts, guidance, and time that he gave for the researcher to learn more

about computational research.

Mr. Darwin F. Reyes, RCh., MSc., the research critic for his indeterminable

efforts for checking even the small wrong details in this research paper. The researcher’s

deepest gratitude for his moral support and efforts.

Mrs. Marilene C. Hipolito, RCh., the research instructor for her guidance during

from the start of this paper.

To all BS Chem 4-A students, for their moral support and motivation for the

researcher.

To Lucas Family, for the financial and moral support, and for being an inspiration

for the researcher.

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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TABLE OF CONTENTS

TITLE PAGE i
APPROVAL SHEET ii
BIOGRAPHICAL DATA iii
ACKNOWLEDGEMENTS iv
LIST OF FIGURES vi
LIST OP APPENDICES viii
LIST OF APPENDIX FIGURES ix
ABSTRACT x

CHAPTER I

BACKGROUND OF THE STUDY 1

RESEARCH OBJECTIVES 4
SIGNIFICANCE OF THE STUDY 5
SCOPE AND LIMITATIONS 6
DEFINITION OF TERMS 6

CHAPTER II

REVIEW OF RELATED LITERATURE 8

CHAPTER III

RESEARCH PARADIGM 31
MATERIALS AND METHODS 32

CHAPTER IV

ABSORPTION DISTRIBUTION METABOLISM EXCRETION 61

BINDING SCORES 71
INTERMOLECULAR FORCES OF ATTRACTION 83

CHAPTER V

SUMMARY OF THE FINDINGS 103

CONCLUSIONS 104
RECOMMENDATIONS 105

REFERENCES 124

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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LIST OF FIGURES

FIGURE PAGE

1 Ocimum sanctum Linn (Sulasi)……………………………………..…. 25

2 Buddleja asiatica (Malasambung)……………………………………... 26

3 Research Paradigm…………………………………………………...... 31

4 M29-NSP9 Complex…………………………………………………... 83

5 M28-NSP9 Complex………………………………………………....... 84

6 M32-NSP9 Complex…………………………………………..…......... 85

7 M8-NSP9 Complex………………………………………...………….. 86

8 M6-NSP9 Complex………………………………………………..…... 87

9 M7-NSP10 Complex…………………………………………….…….. 88

10 M29-NSP10 Complex…………………………………………………. 89

11 M30-NSP10 Complex…………………………………………………. 90

12 M26-NSP10 Complex…………………………………………………. 91

13 M34-NSP10 Complex……………..…………………………………... 92

14 C13-NSP9 Complex……………………………………………….…… 93

15 C29-NSP9 Complex……………………………………………………. 94

16 C30-NSP9 Complex……………………………………………………. 95

17 C22-NSP9 Complex……………………………………………………. 96

18 C23-NSP9 Complex……………………………………………………. 97

19 C2-NSP10 Complex……………………………………………………. 98

20 C8-NSP10 Complex…………………………………………………….99

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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21 C5-NSP10 Complex…………………………………………………..100

22 C29-NSP10 Complex……………………………………………...….101

23 C30-NSP10 Complex………………………………………...……….102

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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LIST OF APPENDICES

Potential Antiviral Properties of Bioactive Compounds and Phytochemicals from

Selected Plants Against SARS-COV-2 Non-structural Proteins (NSP9/NSP10)

Appendix 1: Absorption Distribution Metabolism Excretion using SwissADME

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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LIST OF APPENDIX FIGURES

APPENDIX FIGURE PAGE

1 M29 108

2 M28 109

3 M32 110

4 M8 111

5 M6 112

6 M7 113

7 M30 114

8 M26 115

9 M34 116

10 C13 117

11 C29 118

12 C30 119

13 C22 120

14 C23 121

15 C2 122

16 C8 123

17 C5 124

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)
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ABSTRACT

In December 2019, in Wuhan City, China, there was a cluster of pneumonia cases,

and the disease was first seen in the vendors in a live animal market. The disease is called

COVID-19 and the virus causing this disease is called SARS-CoV-2. The study aims to

determine the potential antiviral property of bioactive constituents from selected plants

which is Buddleja asiatica Lour (Malasambung/Dog Tail), and Ocimum tenuiflorum Linn

(Sulasi/Holy Basil) against NSP9 and NSP10 of SARS-CoV-2. The study includes ADME

analysis to screen the ligands, molecular docking analysis to interact with the ligands and

proteins, and IMFA analysis to visualize the protein-ligand complexes. The results showed

that for NSP9, the 13,28-epoxy-3beta,23-Oisopropylidene-11-oleanene from the

Malasambung with the highest binding score of -7.1 and Sulasi the highest is 16-Hydroxy-

4,4,10,13-tetramethyl-17-(4-methyl-pentyl)-hexadecahydro-cyclopenta[a]phenanthren-3-

one with a score of -6.6. On the other hand for NSP10, the ligands with good scores are

13,28-epoxy-3beta,23-Oisopropylidene-11-oleanene from Malasambung with -10.4, and

Luteolin from Sulasi with a -8.7 binding score. The best IMFA for NSP9 was shown by

Stigmasterol and Tulsinol B. On the other hand, for NSP10 the top ligands with a good

IMFA are Apigenin-&-O-β-Dglucoside and Luteolin. The Philippines has a lot of flora to

explore, the researcher recommends that other plants should be also be looked into further

studies.

Keywords: Non Structural Proteins, SARS-CoV-2, IMFA, Molecular Docking,

Indigenous Plants

Lucas, Ramil S. 2022. POTENTIAL ANTIVIRAL PROPERTIES OF BIOACTIVE COMPOUNDS AND

PHYTOCHEMICALS FROM SELECTED PLANTS AGAINST SARS-COV-2 NON STRUCTURAL
PROTEINS (NSP9/NSP10)