AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV

Abstract

Serious illnesses caused by viruses are becoming the world's most critical public health issues and lead millions of deaths each year in the world. Thousands of studies confirmed that the plant-derived medicines could play positive therapeutic effects on the patients with viral diseases. Since thousands of antiviral phytochemicals have been identified as lifesaving drugs in medical research, a comprehensive database is highly desirable to integrate the medicinal plants with their different medicinal properties. Therefore, we provided a friendly antiviral phytochemical database AVPCD covering 2537 antiviral phytochemicals from 383 medicinal compounds and 319 different families with annotation of their scientific, family and common names, along with the parts used, disease information, active compounds, links of relevant articles for COVID-19, cancer, HIV and malaria. Furthermore, each compound in AVPCD was annotated with its 2D and 3D structure, molecular formula, molecular weight, isomeric SMILES, InChI, InChI Key and IUPAC name and 21 other properties. Each compound was annotated with more than 20 properties. Specifically, a scoring method was designed to measure the confidence of each phytochemical for the viral diseases. In addition, we constructed a user-friendly platform with several powerful modules for searching and browsing the details of all phytochemicals. We believe this database will facilitate global researchers, drug developers and health practitioners in obtaining useful information against viral diseases.

Full text

AVPCD: a plant-derived medicine database of antiviral
phytochemicals for cancer, Covid-19, malaria and HIV
Shahid Ullah1,*, Wajeeha Rahman1, Farhan Ullah1, Anees Ullah1, Gulzar Ahmad1,
Muhammad Ijaz1, Hameed Ullah1, Zilong Zheng2 and Tianshun Gao2,*
1S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
2Big Data Center, The Seventh Afliated Hospital of Sun Yat-sen University, Shenzhen 518107, P. R. China
*Corresponding author: Tel: 86 18126408738; Fax: 86 020-84115962; Email: gaotsh3@mail.sysu.edu.cn
Correspondence may also be addressed to Shahid Ullah. Tel/Fax: 92 15919433631; Email: drskbioch@gmail.com
Citation details: Ullah, S., Rahman, W., Ullah, F. et al. AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19,
malaria and HIV. Database (2023) Vol. 2023: article ID baad056; DOI: https://doi.org/10.1093/database/baad056
Abstract
Serious illnesses caused by viruses are becoming the world’s most critical public health issues and lead millions of deaths each year
in the world. Thousands of studies conrmed that the plant-derived medicines could play positive therapeutic effects on the patients
with viral diseases. Since thousands of antiviral phytochemicals have been identied as lifesaving drugs in medical research, a compre-
hensive database is highly desirable to integrate the medicinal plants with their different medicinal properties. Therefore, we provided
a friendly antiviral phytochemical database AVPCD covering 2537 antiviral phytochemicals from 383 medicinal compounds and 319
different families with annotation of their scientic, family and common names, along with the parts used, disease information, active
compounds, links of relevant articles for COVID-19, cancer, HIV and malaria. Furthermore, each compound in AVPCD was annotated
with its 2D and 3D structure, molecular formula, molecular weight, isomeric SMILES, InChI, InChI Key and IUPAC name and 21 other
properties. Each compound was annotated with more than 20 properties. Specically, a scoring method was designed to measure
the condence of each phytochemical for the viral diseases. In addition, we constructed a user-friendly platform with several powerful
modules for searching and browsing the details of all phytochemicals. We believe this database will facilitate global researchers, drug
developers and health practitioners in obtaining useful information against viral diseases.
© The Author(s) 2023. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/),
which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Introduction
Nature is a unique origin of systems with a wide range of
phytochemical diversity, many of which have fascinating bio-
logical activities and medicinal properties. Phytochemicals are
bioactive, naturally occurring chemical compounds, which are
present in plants and provide health benets to humans (1). It
is present in different parts of the plants, such as in the roots,
stems, leaves, rhizome, owers, fruits or seeds. The plant king-
dom is a great source of potential drugs, and there has been
a signicant role of medicinal plants in recent years. Plant-
based drugs are widely available, less expensive, safe and
efcient with few side effects (2, 3). Phytochemicals benet
plants by performing secondary functions, including assist-
ing in plant growth, protecting plants by activating defense
mechanisms and imparting color, odor and avor to the plants
(4). According to traditional medicinal practices as well as
modern scientic studies, they are useful for medicinal pur-
poses to alleviate diseases and improve human health. These
plants are thought to be rich sources of phytochemicals that
can be used in the synthesis and production of drugs (5, 6).
These phytochemicals, such as avonoid, quinine, quercetin
and terpenoid, perform good biological functions with
many therapeutic activities, including anti-cancer, anti-HIV,
anti-malaria and anti-Covid (7). Each year, tens of millions of
people are infected with different viruses including COVID,
malaria, HIV, cancer-inducing viruses, which cause 571 mil-
lion, 241 million, 37.9 million and 18.1 million infections,
respectively. Commonly used antivirals often have limited
efcacy and serious side effects, while herbal extracts have
been used for medicinal purposes since ancient times and are
known for their antiviral properties and tolerable side effects
(8, 9). The spread of viral diseases is a worldwide concern,
requiring a critical need for the most promising antivirals.
Some viral diseases can be cured with approved antiviral
drugs, but others have no vaccines or drugs available. The
majority of approved antiviral drugs are associated with side
effects, which eventually raise the need for the development
of antiviral based on natural phytochemicals (10, 11). Most
viral diseases, such as HIV, cancer, malaria and Covid-19,
as well as other diseases caused by alphaviruses, aviviruses
and plasmodium, are posing a signicant risk. Coronavirus
disease (COVID-19), caused by a newly identied coron-
avirus, recently became pandemic and severely impacted the
world’s population. Due to viruses’ ability to mutate their
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2Database, Vol. 00, Article IDbaad056
Figure 1. The graphical abstract of the AVPCD.
genomes and become resistant to drugs, developing effective
treatments and antivirals against viruses has become difcult
in the recent years (12–14). Antiviral drugs also have side
effects that affect human health both directly and indirectly.
This leads toward the development of plant-based drugs and
herbal treatments with few side effects (15, 16). Computa-
tional resources are a valuable source of data, expertise and
information in biological research, especially for medicinal
plants due to their different medicinal properties (17). Sev-
eral databases have been published in this eld of research
such as MAPS (18), MPD3 (19), IMPPAT (20) and TIPdb
(21) that have much more phytochemical data. However, we
have presented a special platform for antiviral phytochem-
ical and have collected almost all the data from 1980 to
2021. Previously, we have also published numerous biologi-
cal databases of different research area, which are Co-19pdb,
dbpaf, CGDB, DBPSP and so on. In this work, we have
tried to provide a friendly platform for global researchers,
drug developers, health practitioners and students with very
frequent updates to add in their study and research, which
is a comprehensive collection of 2537 antiviral phytochem-
icals from 383 medicinal plants and 319 multiple families,
including their scientic, family and common names, as well
as their utilized parts, disease information, PubMed IDs or
links of relevant articles, compound summary including 2D &
3D structure, molecular formula, molecular weight, isomeric
SMILES, InChi, Inchikey, IUPIC name and 21 other prop-
erties. We have used different keywords such as ‘Medicinal
plant’, ‘phytochemical’, ‘plant-derived compound’, ‘COVID
related drugs plant’, ‘cancer related medicinal plant’, ‘malaria
medicinal plant’ in several search engines including Google,
Google Scholar, PubMed, Science Direct and Bing for search-
ing. Finally, we have provided a comprehensive database,
which is built in JavaScript, PHP, HTML and CSS, which
will be updated timely. The graphical image Figure 1 is the
stepwise representation of the medicinal plants to nal drugs
and human trial, while Table 1 shows all the statistics of
the data.
Table 1. The number of collected data
AVPCD
Anti-
cancer
Anti-
malarial
Anti-
HIV
Anti-
COVID Others Total
Phytochemicals 319 586 1478 109 45 2537
Medicinal
plants
97 180 84 13 9 383
Family 97 116 84 13 9 319
Result and discussion
Construction of AVPCD
We integrated the data from multiple sources, including
PubMed, Google, Google Scholar and so on. We have used
various keywords such as ‘Antiviral Medicinal plants’, ‘Antivi-
ral Phytocompound’, ‘Antiviral Herbal medicine’, ‘Antivi-
ral Traditional medicine’ and ‘databases of Antiviral Phy-
tocompound’ to search and retrieve published antiviral-
phytocompound-related data with the help of literature
database of PubMed (http://www.ncbi.nlm.nih.gov/pubmed).
To circumvent missing data, we have manually collected
the latest data from The New Phycologist (https://nph.
onlinelibrary.wiley.com/), Bioresource Technology (https://
www.elsevier.com/journals/bioresource-technology),
Nucleic Acids Research (NAR) (https://academic.oup.com/n
ar) and journal of Genomics, Proteomics & Bioinformatics
(GPB) (https://www.journals.elsevier.com/genomics-proteomi
cs-and-bioinformatics), which are the leading research jour-
nals on database issue. To obtain antiviral phytochemicals of
high quality, we collected only the experimentally validated
compounds and removed the ones with broken links. Multi-
ple programming languages including PhP, MYSQL, HTML,
CSS and JavaScript have been used to construct the database.
Figure 2 depicts all of the steps for collecting the data and
creating the database, both in terms of colors and aesthetics.
Finally, we supplied to the scientic community a compres-
sive antiviral phytochemical research database that is simple
to use and will be updated over time.
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Database, Vol. 00, Article IDbaad056 3
Figure 2. Color-wise and graphical representation of the collection of antiviral phyto-compounds and construction of AVPCD.
Usage of the AVPCD database
Search option of AVPCD
AVPCD is designed in an easy and user-friendly way for
searching and browsing the data. To know more in depth,
users could search ve classic examples including ‘quercetin’,
‘Sedum sarmentosum’, ‘Aseraceae’, ‘Lobelia’ and ‘Anti HIV’
by clicking ‘compound’, ‘scientic name’, ‘Family name’,
‘Local Name’ and ‘Disease’ buttons, as shown in Figure 3A,
respectively. Users could get the result by selecting the com-
pound of interest in Figure 3B. Further clicking the highlighted
AVPCD ID will bring the user to the nal result, shown
in Figure 3E. For special search, we provided the ‘Advance
Search’ option, shown in Figure 3C, with xed ‘Anti-Cancer’
as an example, and on further click it will open a new win-
dow with the compound list, as in Figure 3D. Clicking the
compound of interest will link to a new page with all required
knowledge of this compound, such as scientic, local and
common name from obtained plants, utilized part, disease
for used, original resources with short introduction of the
needed plants, compound summary, compound score, 2D
and 3D structure, molecular formula, molecular weight, iso-
meric SMILES, InChI, InChI Key, IUPIC name and 21 other
properties, shown in Figure 3E.
Browse option of AVPCD
Three different browse options are available to browse the
AVPCD data. To obtain the whole result of each antivi-
ral, users can click on the browse option and then directly
get all the needed information by clicking any antiviral shown
in Figure 4A. Furthermore, we gave the image expression
browse option shown in Figure 4C, and clicking the required
category will lead to the new window and nal result. We
also xed the browse option by top 10 rich compound image
with formula shown in Figure 4C. To make it easier and more
authentic, we provided several options on the main bar of
the database, including the ‘Usage’ showing the detail with
visual image expression of database, ‘statistics’ displaying the
statistics of the database, ‘download’ giving all the data for
scientic research only after publishing the article and ‘use-
ful links’ presenting the published databases of this research
area with two buttons. Clicking the active button will give the
database while the dead button will bring users to the broken
database article (Figure 4D).
The biological activities
We analyzed the bioassays of top 10 compounds, includ-
ing Alkaliods, Quercetin, Saponins, Flavonoids, Tanins,
Triterpenoids, Steriod, Caffeic Acid, Kaempferol and Gal-
lic Acid. We checked the total biological activities as well
as specic mentioned antiviral effects, among them. Alka-
liods, Flavonoids, Steriods and Triterpenoids are the more
active compounds that have more correlation with dis-
eases (Figure 5A). Moreover, we have specied the antiviral
activity, anticancer, antimicrobial, antimalarial activity of
the top 10 compounds, in which Alkaliods are the most
useful compounds for all diseases and highly active for anti-
cancer antimicrobial, antiviral and antimalarial. Quercetin is
the second active compound that can be used in anticancer
antimicrobial, antiviral and antimalarial. The details of all top
compounds are shown in Figure 5B.
Statistics of the AVPCD
In the current work, we have a comprehensive collection of
total 2537 antiviral phytochemicals from a total of 383 medic-
inal plants and total 319 multiple families, including their
scientic, family and common names, as well as their uti-
lized parts, disease information, active compounds, PubMed
IDs or links of the relevant articles. We also compared the
numbers of phytochemical, species and family among the ve
classications, in which ‘anti HIV’ is on the top (Figure 6A).
Figure 6B shows the percentage of all antiviral phytochemical,
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4Database, Vol. 00, Article IDbaad056
Figure 3. Usage of AVPCD. (A) The simple search with ve search options. (B) The compound list by the selected option in simple search. (C) The
advanced search of the AVPCD. (D) The compound list by the advanced search. (E) All the needed and nal data of the searched query.
while Figure 6C presents degree of use for different usable
parts of the medicinal plants.
Aims of the AVPCD database
The AVPCD intended to collect information in a uniform
manner regarding all published experimental antiviral phy-
tochemicals, including plant species, their scientic local and
common names and areas, especially the bioassays of antiviral
phytochemical compounds. This database includes informa-
tion on the species taxonomy, distribution, ecology, collection
records, analytical data and references to previous studies and
will be updated on a regular basis with new ndings and more
information. Further, we have focused on creativity, consis-
tency and clarity for which we are working on voice interface
designing, regional language search option, as well as API’s, as
we previously published multiple datasets on various research
areas in highly referenced international journals, including a
database of circadian genes in eukaryotes (CGDB) in Nucleic
Acids Research (22), cancer research database (CRDB) in
JMIR Cancer (23), databases on phosphorylation animal and
fungi (DBPAF) in Scientic Report (24), Latest Database of
Protein Research (LDBPR) in Journal of Bioinformatics and
Systemic Biology (25), database for protein phosphoryla-
tion sites in prokaryotes (dbPSP), in Database (Oxford) (26),
COVID-19 Pandemic Database (CO-19PDB) in Computer
Methods Programs and Biomedicine Updates (27), Database
relevant to Human Research (DBHR) in Future Science OA
(28). In all, we have provided a huge platform of 19 databases
of different research area named ‘Home of all Biological
Databases’ (HABD) (29, 30) (www.habdsk.org) in Table 2,
which gave free access for global scientic community. There-
fore, we felt to give comprehensive databases in this eld of
research as well; for that, AVPCD aims to provide wonderful
insights for researchers with well-gathered previously pub-
lished work in one platform. We tried to provide access to data
from sources that are difcult to locate. AVPCD gives details
that may not have been published before on such easy and
friendly way in the open literature. AVPCD monitored and
updated the dead and broken databases and have provided a
separate page with two moods. Clicking the active mood will
give the database and dead mood will bring the articles with
more knowledge, evidence or citations.
The advantages of AVPCD against other databases
Although many useful databases have been published in
the phytochemical research area, none of them is specially
designed for antivirals. In order to accomplish this, we
attempted to develop a comprehensive special platform for
antiviral data and to allow easy access to the scientic com-
munity with rapid updates. We have provided all antiviral
compound information that has not previously been pub-
lished in such an easy manner. Regarding previous databases,
some of them only supplied phyto-compounds, some plants
and some parts, and the majority of them had limited antiviral
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Database, Vol. 00, Article IDbaad056 5
Figure 4. Usage of the database. (A) The browse option by antiviral category. (B) Browse by disease-wise image expression. (C) Browse page of the
AVPCD based on the top 10 rich compound images and formula. (D) Useful links to the relevant databases with two modes.
Figure 5. The top 10 compounds with different biological activities. (A) The bioassays of top 10 compounds. (B) The bioassays of mentioned antiviral
compounds in AVPCD.
data, so we felt that in this pandemic, we should give a sepa-
rate and dedicated platform specically for viral diseases. Our
database solely contains information about antiviral diseases
and compounds.
AVPCD phyto-compounds scoring system
Various scoring systems have been presented in published
work, for example, molecular docking scoring of some
phyto-compounds (31–33), experimental work evidence of
the top 10 compounds, on the basis of which we have given
the special scoring system and have presented it in AVPCD;
we have used the following formula and have cross checked all
the data with published work. Artemisinins ranked rst in our
score, and a Chinese scientist was awarded the Nobel Prize in
2016 for it (34–36), followed by keampferol, used to treat
a variety of disorders (37–40), Chlorogenic acids (41–43),
Lupeol (44–46), Oleanolic acid (47–49), Robusta avone,
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6Database, Vol. 00, Article IDbaad056
Figure 6. The statistics of AVPCD, (A) The number of antiviral phytochemicals, species and family. (C) The percentage of antiviral phytochemical. (D) The
number of all usable parts of medicinal plants.
Table 2. All databases of the HADB site
Db title Databases links Databases category Status
1) Compendious databases
DBHR https://www.habdsk.org/dbhr Human (28)
LDBPR https://www.habdsk.org/ldbpr Protein (25)
Co-19PDB https://www.habdsk.org/co-19pdb Covid-19 (27)
CRDB https://www.habdsk.org/crdb Cancer and Covid (23)
Edbco-19 https://www.habdsk.org/edbco-19 Covid-19 (64)
FDBC https://www.habdsk.org/fdbc Fungi (65)
DBPR https://www.habdsk.org/db-pr Plant Submitted
DBBT https://www.habdsk.org/dbbt Biological tools Ongoing
CO-19PDB 1.0 https://www.co-19pdb.habdsk.org/ Covid-19 Ongoing
CBDB https://www.habdsk.org/cbdb Biological DB Ongoing
DBFBPA https://www.habdsk.org/db-fbpa Fungus, Bacteria, Protozoa Ongoing
BDSR https://www.habdsk.org/bdsr Biological Db Ongoing
CDB-PTMS https://www.habdsk.org/cdb-ptms PTMs Ongoing
CHCRD https://www.habdsk.org/chcrd Cancer Submitted
2) Phyto-databases
AVPCD https://avpcd.habdsk.org/ Antiviral This one
HADB https://hadb.habdsk.org/ Hyper-accumulators ———
MPDB https://www.mpdb.habdsk.org/ Medicinal plant ———-
PTDB https://www.ptdb.habdsk.org/ Phytotoxin ———
3) Others databases
PBDB https://pbdb.habdsk.org/ Plastic biodegrading ———-
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Database, Vol. 00, Article IDbaad056 7
Figure 7. The future direction of the antiviral phytochemicals.
Cucurbitacins (50–53), Rutinosid (54, 55), Morelloavone
(56–58), Betulinic (59–61) and Hinokiavone (62, 63); Jac-
card similarity formula is used to measure the correlation
between any two phyto compounds (e.g. 𝑖and 𝑗) based on
the overlap in the same study. The Jaccard similarity between
𝑖and 𝑗 can be calculated as
𝑝𝑖𝑝𝑗𝑖𝑃𝑗
𝑖𝑃𝑗𝑖𝑃𝑗
𝑖𝑗𝑖𝑃𝑗
where𝑖, 𝑗and 𝑖𝑗 represent the number of the stud-
ies in 𝑖, 𝑗 and their overlap, respectively. For a single Phyto-
compound, its Jaccard similarity matrix of combination of all
the data was integrated as





𝑝1𝑝1 𝑝1𝑝𝑖
   𝑝1𝑝𝑛

𝑝𝑖𝑝1 𝑝𝑖𝑝𝑖
 
𝑝𝑛𝑝1 𝑝𝑛𝑝𝑖
 𝑃𝑖𝑝𝑛

 𝑝𝑛𝑝𝑛





Using the Jaccard matrix, we measured the strength of any
Phyto-compound 𝑖 as
pi𝑛
𝐽=1 𝑃𝑖𝑗
𝑛
𝐽=1,𝑘=1 𝑝𝑗𝑝𝑘     
By combination of all phyto-compounds in one nal score,
the signal score of any phyto-compound i could be dened as
𝑠𝑐𝑜𝑟𝑒  𝑛

𝑗=1 𝑝𝑗𝑝𝑗
where 𝑝𝑗 represents the signal score of the disease in the
phyto-compound𝑗.
Future direction
Many traditional medicines and phytochemicals are directly
utilized to treat various ailments; however, the majority of
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8Database, Vol. 00, Article IDbaad056
them have efcacy and safety concerns. In Figure 7, we
depict the future trend for antiviral phytochemicals that can
be used and will be more advantageous for modern medi-
cations. Interferon and ribavirin, for example, are efcient
in vitro against most viruses but are frequently unsuccess-
ful in humans. Today’s antiviral medications (3, 4) address
only a subset of viruses, including HIV, herpes viruses such as
HSV, human cytomegalovirus (hCMV), varicella zoster virus
(VZV), inuenza viruses and hepatitis viruses. There is cur-
rently no approved treatment for many types of viruses, and
vaccination is conned to hepatitis A, mumps and varicella.
Furthermore, these drugs are frequently expensive and inef-
fectual due to viral resistance, and they induce side effects.
Keeping this in mind, natural-based pharmacotherapy may
be a viable option for treating viral infections. As a result,
more research into antiviral phytochemicals is required, with
a focus on drug delivery applications in overcoming many bio-
logical obstacles that exist for antiviral medicines to success-
fully reach their intended site(s) of action. The current study
focuses on the antiviral capabilities of herbal extracts and
bioactive ingredient isolates derived from medicinal plants, as
well as initiatives to improve their administration.
Conclusion
A biological database is a collection of tools for storing, orga-
nizing and retrieving biological data and other types of infor-
mation so that it may be conveniently examined, controlled
and amended. A number of articles have been published in
this eld of research, each of which has its own collocation of
data based on function, use, technical factors and species. For
such works, we have provided a well-managed database that
aimed to maintain medicinal plants and other phytochemical-
tolerant plants; timely identication is required in order to
investigate their unique physiological systems and take benet
of their unique characteristics. Further, our database provides
statistical support for the existence of antiviral phytochemi-
cal and medicinal plants in global, regional and local oras
based on disease concentrations. In addition, we have pro-
vided every single compound summary including 2D and
3D structure, molecular formula, molecular weight, isomeric
SMILES, InChI, InChI key, IUPAC name and 21 other proper-
ties; we have collected almost all the data with their relevant
knowledge and have provided a separated page with a short
introduction and have updated or removed all broken and
unveried data. Furthermore, AVPCD offers two search and
three browse options in an easy and friendly nding manner,
and will be updated in time, that can be access through this
link https://www.avpcd.habdsk.org/.
Availability of data and materials
These data will be available under the journal rule and
regulation.
Author’s contribution
Dr Shahid Ullah and Dr Tianshun Gao supervised the project.
Ms Wajeeha Rahman, Dr Anees Ullah, Mr Farhan Ullah, Mr
Hameed Ullah, Mr Gulzar Ahmad and Mr Muhammad Ijaz
collected and veried the data carefully. All authors reviewed
the manuscript and agreed to submit. Further, Dr Shahid Ullah
has the right to manage, update and give all feedback of the
database in the future.
Funding
This project is supported by National Natural Science Foun-
dation of China (32100434) and Shenzhen’s introduction of
talents and research start-up (392020).
Conict of interest statement
None declared.
Acknowledgements
In order to avoid future conict and plagiarism, The
AVPCD database has been uploaded at https://www.avpcd.
habdsk.org/.
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