International Journal of Chem-informatics Research vol 2 issue 2

International Journal of
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IJCR
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Cheminformatics Research
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review process. It is designed to create interest among researchers in this field which deal with the use of
computer and informational techniques applied to wider range problems in the field of chemistry. The main
function of this journal is in the areas of topology, chemical graph theory, information retrieval and data
mining in the chemical field. Cheminformatics can also be used in chemical and allied industries in several
other forms. Journal aims to publish original, high quality papers that are peer-reviewed by our expert
editorialteamtoensurethepublicationof onlygood qualitypapers.
Focus andScopeoftheJournal
 Chemical databases
 Drug discovery
 Computer-assisted synthesis design
 Computer-assisted molecular design
 Organizing chemical facts into databases
 Molecular modeling
 Structure generators
 Modeling 3D structures
 Database mining
 Graph mining
 Molecule mining
 Sequence mining
 Digital libraries
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Swami Shraddhanand College, Department of
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Dr. Monika Gupta
Department of Chemistry,
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Jammu, India
Dr. P. V. Singh
Department of Chemistry, Institute of
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Department of Chemistry/Polymer and Rubber,
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Navin Fluorine International Limited,
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Department of Chemistry (DST-FIST-PURSE
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Dishman Pharmaceuticals and Chemicals
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Emami Limited, India
Dr. Susarla Venkata Ananta Rama Sastry
MVGR College of Engineering, Vizianagaram,
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From the Editor's Desk
Dear Readers,
We would like to present, with great pleasure, the inaugural volume of a new scholarly
journal, International Journal of Cheminformatics Research. This journal is part of the
Applied Sciences, and is devoted to the scope of present chemical synthesis and chemical
reactions issues, from theoretical aspects to application-dependent studies and the validation of emerging
technologies.
This new journal was planned and established to represent the growing needs of Cheminformatics Research
as an emerging and increasingly vital field, now widely recognized as an integral part of scientific and
technical investigations. Its mission is to become a voice of the Cheminformatics Research Science
community,addressing researchersandpractitionersinthisarea.
The core vision of International Journal of Cheminformatics Research in Journals Pub is to propagate novel
awareness and know-how for the profit of mankind ranging from the academic and professional research
societies to industry practitioners in a range of topics in Cheminformatics Research in general. Journals
Pub acts as a pathfinder for the scientific community to published their papers at excellently, well-time &
successfully.
International Journal of Cheminformatics Research focuses on original high-quality research in the realm
of Chemical databases, Drug discovery, Computer-assisted synthesis design, Computer-assisted molecular
design,Structuregenerators, Modeling3D structures,Database mining,Digitallibrariesandmany more.
Many scientists and researchers have contributed to the creation and the success of the Cheminformatics
Research community. We are very thankful to everybody within that community who supported the idea of
creating an innovative platform. We are certain that this issue will be followed by many others, reporting
newdevelopmentsinthefieldofCheminformaticsResearch.
This issue would not have been possible without the great support of the Editorial Board members, and we
would like to express our sincere thanks to all of them. We would also like to express our gratitude to the
editorialstaffofJournalsPub,who supported us ateverystageoftheproject.
It is our hope that this fine collection of articles will be a valuable resource for Cheminformatics Research
readers andwillstimulatefurtherresearchintothevibrantareaofCheminformaticsResearch.
PuneetMehrotra
ManagingDirector

1. Structure-Based Drug Design for Therapeutic Application
Aruna Singh 1
2. A Short Note on: Computer-Aided Molecular Design
Zeanut Akoijam 3
3. Understanding Chemical Database Tools: A Guide to Beginners
Amit Agnihotri 6
4. Brief Introduction to Cheminformatics
Dayananda Singh Konjengbam 9
5. Developmental Process of New Medicines: A Brief Insight
Varun Singh Parmar 13
Contents

IJCR (2016) 1-2 © JournalsPub 2016. All Rights Reserved Page 1
International Journal of Cheminformatics Research
Vol. 2: Issue 2
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Structure-Based Drug Design for Therapeutic Application
Aruna Singh*
Department of Engineering and Technology, Indira Gandhi National Open University, New
Delhi, India
ABSTRACT
Computational methods have paved a long way in identification and characterization of
molecules with special reference to drugs, protein molecules and other medicinal purposes.
Commonly applied computational techniques include quantitative structure-activity,
quantitative structure-property relationships ligand-based drug design and structure-based
drug design (drug-target docking). Here, is provided an overview of the structure-based drug
designing and its applications.
Keywords: computational methods, docking, drug designing, structure-based drug design
BACKGROUND
Computer-based techniques have shown
great advancements and applications in
different areas of basic and applied
research. These techniques utilize a
computer and diverse array of software
packages to carry out multiple aspects. The
strategies carried out depend largely on the
pre-existing data and information that are
stored in large databases which are
commercially available. Some of the
databases are freely accessible while there
are others in which some part of the data
can be accessed free of cost but other parts
of the data are chargeable. Computer-aided
drug designing is an innovative tool that
has helped in facilitating the design and
discovery of several therapeutic molecules.
Earlier, drug designing used to be a time
taking procedure requiring lot of resources
and huge manpower. Now, with the help
of computational power, it has become
possible to combine the biological and
chemical knowledge in streamlining drug
discovery, designing and development.
The varying computational tools and
resources have made it easier for the
storage, management, visualization,
examination and modeling of compounds.
The in-silico approach assists in
facilitating hit identification, hit-to-lead
selection, optimize the absorption,
distribution, metabolism, excretion and
toxicity profile and avoid safety issues [1].
The methods used in drug designing are
mostly structure based or ligand based.
The former includes ligand docking,
pharmacophore, and ligand design
methods. These methods are based on
high-throughput screening. The ligand-
based method uses ligand information for
prediction of activity based on the
similarity/dissimilarity consensus when
compared to already known active ligands
[2].
Structure-based drug design also referred
as target-based drug design involves
docking. To explain it further, in structure-
based drug design, ligand binds to its
receptor molecule on the target protein.
This method helps to identify, characterize
and standardize optimum candidates of
drugs or other medicines. This is done by
carefully assessing and performing

IJCR (2016) 3–5 © JournalsPub 2016. All Rights Reserved Page 3
Vol. 2: Issue 2
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A Short Note on: Computer-Aided Molecular Design
Zeanut Akoijam*
Department of Chemistry, Manipur University, Manipur, India
ABSTRACT
Computational techniques are gaining large popularity owing to their power that combines
chemical and biological space to streamline different areas of research and development.
Computer-aided molecular design helps in identifying, characterizing small and large
molecules and also helps to modify them for required purpose.
Keywords: computer-aided molecular design, molecular graphics, molecular mechanics,
quantum mechanics
BACKGROUND
Computer-aided molecular design is of
great significance due to its role in
deciding which molecules can be useful
for a given purpose. Computer-aided
molecular design involves molecular
graphics and theoretical calculations [1].
Several databases are available that are
crucial in the development of computer-
aided molecular designing. These
databases contain vast collection of data
and information pertaining to different
molecules, their structure, binding
affinities, etc. One of the main databases is
the Cambridge Structural Database (CSD),
established in 1965 that stores data related
to small-molecular organic, metal-organic
crystal structures, polymer X-ray and
neutron diffraction of above 70,000
compounds [2, 3]. Other database such as
Protein Data Bank (PDB) from
Brookhaven National Laboratory contains
information about macromolecules like
protein and nucleic acids. The PDB is laid
by Worldwide Protein Data Bank
Foundation and provides data including
secondary and tertiary structures of
proteins and nucleic acids, their
sequences, active site residues, etc. [4].
Many other databases are also there that
are either freely accessible or are
commercially available.
MATERIALS AND METHODS
Molecular Graphics
The molecular graphics are exceedingly
useful tools for visualizing and examining
the three-dimensional structure of
molecules. These tools help the biologists
and chemists to understand how the
molecules react and interact. The larger
the molecule, the more difficult it is to
examine and understand it. Molecular
graphics is importantly used for
visualizing large macromolecules such as
proteins.
Molecular graphics require a computer
system and software packages to function.
Some of the widely used packages include
Insight II from Biosym, Quanta from
Molecular Simulations Inc. and Sybyl
from Tripos [5–7]. These software
packages are commercially available and
are also equipped with other facilities
relating to quantum mechanics and
molecular dynamics.
Molecular graphics work in different
ways: it helps to construct a molecule on

IJCR (2016) 6–8 © JournalsPub 2016. All Rights Reserved Page 6
Vol. 2: Issue 2
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Understanding Chemical Database Tools: A Guide to Beginners
Amit Agnihotri*
Department of Chemical Engineering, ITM, Gwalior, India
ABSTRACT
Chemical database have become an important part in chemical sciences. It helps the
scientists to search and analyze data on a large scale for varying purposes. Herein, we have
briefed the concept of chemical databases and their role in chemistry. This brief review will
help the beginners and graduate students improvise their knowledge in this field.
Keywords: chemical, database, search tool
BACKGROUND
Computers and internet have become an
integral part of research. Whatever
scientific information one wants to have,
can be easily explored by simply typing
keywords related to the concerned topic,
on the search bar of internet search
engines. Commonly used search engine is
the Google Scholar which explores the
information through the scientific
literature. Wikipedia is the most
extensively searched encyclopedia that
quickly provides elementary information
for beginners [1]. However, search
engines provide only a small part of the
related contents. To obtain a detailed and
thorough literature review, additional
search options are required.
Chemical databases contain a large source
of chemical information. Several chemical
databases of both commercial and free
access types are available. There are some
databases which are available only
through commercial sources, while there
are others that are commercial but parts of
them are available as free access on
internet. Some other databases are of
topical concern e.g., chemical weapons
[2]. They represent big repositories from
where large data of journals, books,
conferences, workshops, patents,
symposiums and related sources can be
easily retrieved. These chemical databases
are great tools for storing and analyzing
huge collection of data. Some of the useful
chemical databases are briefed below:
Cambridge Structural Database (CSD)
The CSD, established in 1965, is the
world’s repository for small-molecular
organic and metal-organic crystal
structures [3]. It also stores several data of
X-ray and neutron diffraction analysis.
This tool has been of great resource to
scientists across the world.
ChEMBL and Chemical Entities of
Biological Interest (ChEBI)
Established by the European
Bioinformatics Institute (EMBL-EBI),
UK, ChEMBL stores data relating to
binding, functional and ADMET
bioactivity [4]. The ChEBI stores small
chemical compounds.
TOXNET
It comprises a collection of databases on
hazardous chemicals, drugs, toxic releases,
environment and diseases, occupational
health and safety. It is developed by
Toxicology and Environmental Health

Vol. 2: Issue 2
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Brief Introduction to Cheminformatics
Dayananda Singh Konjengbam*
Department of Chemistry, Bundelkhand University, Jhansi, India
ABSTRACT
Cheminformatic research is the science of computational and informational techniques to
solve problems related to chemistry, physics, biology, biochemistry, statistics etc.
Cheminformatics involves collection of many different chemical information and data,
creating new designs, organizing the collected data and related information, management
and analysis of the data. Several tools and computational software are utilized in this. A brief
overview is given here to describe cheminformatics and its need and importance for today’s
research.
Keywords: cheminformatics, ChemDraw, computational science, drug discovery,
information technology
INTRODUCTION
The origin of cheminformatics dates back
in 1990’s when F. K. Brown for the first
time introduced this term while
highlighting the importance of information
technology and management in drug
discovery process [1–3].
‘Cheminformatics’ also referred as
‘Chemiinformatics’ or
‘Chemoinformatics’ or ‘Chemical
informatics’ or in some cases ‘Chemical
information’ is a distinct branch that deals
with computational molecular sciences.
This branch of science deals with chemical
information contained in 2-dimensional
and 3-dimensional structures of chemical
substances. Cheminformatics is actually a
multidisciplinary area that uses
computational and informational
techniques to understand various problems
of different scientific fields’ viz., biology,
chemistry, physics, mathematics,
biochemistry, statistics and informatics [3,
4].
Cheminformatics comprise design,
creation, organization, visualization,
analysis, management, recovery,
propagation, and use of chemical
information [2, 4]. Brown defined it as
"the mixing of those information resources
to transform data into information and
information to knowledge for the intended
purpose of making better decisions faster
in the area of drug lead identification and
optimization" [1]. Later, in 2006, M. Hann
and R. Green defined the term
cheminformatics as ‘a new name for an old
problem’ [5, 6]. Chemists generate huge
amounts of chemical data that can be
maintained and easily accessed using
cheminformatics. Over 45 million
chemical compounds are known and the
number is likely to increase at an average
rate of one million per year. A proper
database is created wherein these chemical
data are stored and retrieved whenever
required. This process becomes feasible
using the science of cheminformatics.
Stages in Cheminformatics
Chonde in 2014 described the stages of
cheminformatics to include capturing,
storing and mining of data. Essentially, 3

Vol. 2: Issue 2
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Developmental Process of New Medicines: A Brief Insight
Varun Singh Parmar
Department of Pharmacy, Baba Mast Nath University, Rohtak, Haryana, India
Background
Scientific advancements have enabled
greater understanding of diseases at
molecular level. With the aid of research
and development, new medicines are
growing from time to time. But
development of medicines is a long, time-
consuming and highly complicated
process. On an average, it takes nearly ten
years for a medicine to complete the long
process of development before it is
introduced into the market for
consumption. Clinical trials alone take 6-7
years on average. The whole series of
steps involved during the development of a
medicine determines its degree of success
after it is being introduced into the market.
Here, a brief insight of the regulatory and
pre-marketing steps that occur to ensure a
successful launch of a medicine is
described.
There exist thousands of compounds that
can be potential candidates for
development as new medicines. Several
tests are undertaken against large number
of diseases to find out the possible medical
benefits of these compounds. After
preliminary testing, however, only a small
number of compounds look promising and
call for further study. The testing of the
compound(s) includes taking into
consideration the following
characteristics[1]
:
(1) How it is absorbed or metabolized and
excreted in/out of human body.
(2) Its mechanism of action.
(3) The ideal dosage for use.
(4) The route of exposure (oral or
intravenous).
(5) Possible side-effects or toxicity.
(6) Any specificity (gender-wise, race or
ethnicity).
(7) How it interacts with other compound
or drugs.
(8) Its effectiveness as compared with
similar compound or drugs.
Preclinical Research
Prior to testing in humans, it is important
to find out the possibility of any toxic
effects of the compound. Pre-clinical
research includes testing the compound
both in vitro and in vivo. The former
method involves testing the compound on
human cells cultured under laboratory
conditions and evaluating the toxicity by
various biochemical techniques.[1,2]
Under
in vivo approach, the compound is injected
to in-house bred mice or rats or any related
mammal. The animals are kept under
observance for any physical signs of
toxicity and their tissues/cells analyzed by
histochemical, immunological and
biochemical tools.
Clinical Research
Though preclinical research provides
information about a compound’s safety, it
is not a substitute for studies of ways the
particular compound will interact within
the human body. ‘Clinical research’
involves studies and/or trials that are done
in people. A clinical research study is
designed in such a way keeping in mind
what is to be accomplished from the
compound in question. A specific protocol
is designed for this. Afterwards,
Investigational New Drug Process (IND) is
initiated, a mandatory process that has to
be carried out prior to initiating the clinical
research. Clinical trials follow a typical

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