International Journal of Cheminformatics - Vol 2_Issue 2

International Journal of

Cheminformatics Research

IJCR

Jul–Dec 2016

Mechanical Engineering

Electronics and Telecommunication Chemical Engineering

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Technologies« International Journal of Digital Electronics« International Journal of Digital Communication and Analog

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Computer Science and Engineering « International Journal of Wireless Network Security« International Journal of Algorithms Design and Analysis« International Journal of Mobile Computing Devices« International Journal of Software Computing and Testing« International Journal of Data Structures and Algorithms

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« International Journal of Solid State Materials« International Journal of Optical Sciences

Physics

« International Journal of Renewable Energy and itsCommercialization

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Civil Engineering« International Journal of Water Resources Engineering« International Journal of Concrete Technology« International Journal of Structural Engineering and Analysis« International Journal of Construction Engineering and

Planning

Electrical Engineering« International Journal of Analog Integrated Circuits« International Journal of Automatic Control System« International Journal of Electrical Machines & Drives« International Journal of Electrical Communication

Engineering« International Journal of Integrated Electronics Systems and

Circuits

Material Sciences and Engineering « International Journal of Energetic Materials« International Journal of Bionics and Bio-Materials« International Journal of Ceramics and Ceramic Technology« International Journal of Bio-Materials and Biomedical

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Engineering

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« International Journal of Machine Design andManufacturing

« International Journal of Mechanical Dynamicsand Analysis

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Biomaterials« International Journal of Plant Biotechnology« International Journal of Molecular Biotechnology« International Journal of Biochemistry and Biomolecules« International Journal of Animal Biotechnology and

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International Journal of Cheminformatics Research aims to serve as a platform for the propagation of

innovative ideas and research in entire areas of Cheminformatics. All manuscripts go through a rigorous peer

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

editorial team to ensure the publication of only good quality papers.

Focus and Scope of the Journal 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

International Journal of Cheminformatics Research is published twice a year (bi-annual) by JournalsPub- is

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INTERNAL MEMBERS

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ChairmanMr. Puneet Mehrotra

Managing Director,JournalsPub,

New Delhi

Hidam Renubala

Ankita Singh

Deepika Bhadauria

Rekha Rani

Commissioning Editors

Dr. Chhavi Goel

Manisha Dhoble

EDITORIAL BOARD MEMBERS

Dr. Yogesh Kumar SharmaSwami Shraddhanand College, Department of

Chemistry, University of Delhi, New Delhi, India

Dr. Monika GuptaDepartment of Chemistry,

University of Jammu, Jammu, India

Dr. P. V. SinghDepartment of Chemistry, Institute of

Technology & Management,Uttar Pradesh, India

Dr. Sandeep RaiDepartment of Chemistry/Polymer and Rubber,

Shroff S.R. Rotary Institute of Chemical Technology, Gujarat, India

Dr. Kishore DasariNavin Fluorine International Limited,

India

Dr. Kaman SinghDepartment of Chemistry (DST-FIST-PURSE Sponsored) Centre of Excellence (U.P. Govt., UGC-DRS (I) –SAP Sponsored Department)Faculty of Science, University of Lucknow,

Lucknow, India

Dr. Ajit Manharlal BhavsarDishman Pharmaceuticals and Chemicals

Limited, Ahmedabad, India

Dr. Satyabrata MohapatraEmami Limited, India

Dr. Susarla Venkata Ananta Rama SastryMVGR College of Engineering, Vizianagaram,

Andhra Pradesh, India

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 researchers and practitioners in this area.

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, Structure generators, Modeling 3D structures, Database mining, Digital libraries and many 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

new developments in the field of Cheminformatics Research.

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

editorial staff of JournalsPub, who supported us at every stage of the project.

It is our hope that this fine collection of articles will be a valuable resource for Cheminformatics Research

readers and will stimulate further research into the vibrant area of Cheminformatics Research.

Puneet Mehrotra

Managing Director

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 BeginnersAmit Agnihotri 6

4. Brief Introduction to CheminformaticsDayananda Singh Konjengbam 9

5. Developmental Process of New Medicines: A Brief InsightVarun 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


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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


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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

IJCR (2016) 9-12 © JournalsPub 2016. All Rights Reserved Page 9


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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

IJCR (2016) 13-15 © JournalsPub 2016. All Rights Reserved


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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



IJCR

Jul–Dec 2016

Mechanical Engineering

Electronics and Telecommunication Chemical Engineering

Architecture

Office No-4, 1 Floor, CSC, Pocket-E,Mayur Vihar, Phase-2, New Delhi-110091, India

E-mail: [email protected]

¬ International Journal of Thermal Energy andApplications

¬ International Journal of Production Engineering¬ International Journal of Industrial Engineering

and Design¬ International Journal of Manufacturing and

Materials Processing¬ International Journal of Mechanical Handling and

Automation

« International Journal of Radio Frequency Design« International Journal of VLSI Design and Technology« International Journal of Embedded Systems and Emerging

Technologies« International Journal of Digital Electronics« International Journal of Digital Communication and Analog

Signals

« International Journal of Housing and Human SettlementPlanning

« International Journal of Architecture and InfrastructurePlanning

« International Journal of Rural and Regional PlanningDevelopment

« International Journal of Town Planning and Management

Applied Mechanics

5 more...

1 more...

2 more...2 more...

5 more...

Computer Science and Engineering « International Journal of Wireless Network Security« International Journal of Algorithms Design and Analysis« International Journal of Mobile Computing Devices« International Journal of Software Computing and Testing« International Journal of Data Structures and Algorithms

Nanotechnology« International Journal of Applied Nanotechnology« International Journal of Nanomaterials and Nanostructures« International Journals of Nanobiotechnology

« International Journal of Solid State Materials« International Journal of Optical Sciences

Physics

« International Journal of Renewable Energy and itsCommercialization

« International Journal of Environmental Chemistry« International Journal of Agrochemistry« International Journal of Prevention and Control of Industrial

Pollution

Civil Engineering« International Journal of Water Resources Engineering« International Journal of Concrete Technology« International Journal of Structural Engineering and Analysis« International Journal of Construction Engineering and

Planning

Electrical Engineering« International Journal of Analog Integrated Circuits« International Journal of Automatic Control System« International Journal of Electrical Machines & Drives« International Journal of Electrical Communication

Engineering« International Journal of Integrated Electronics Systems and

Circuits

Material Sciences and Engineering « International Journal of Energetic Materials« International Journal of Bionics and Bio-Materials« International Journal of Ceramics and Ceramic Technology« International Journal of Bio-Materials and Biomedical

Engineering

Chemistry « International Journal of Photochemistry« International Journal of Analytical and Applied Chemistry« International Journal of Green Chemistry« International Journal of Chemical and Molecular

Engineering

« International Journal of Electro Mechanics andMechanical Behaviour

« International Journal of Machine Design andManufacturing

« International Journal of Mechanical Dynamicsand Analysis

« International Journal of Fracture and damageMechanics

« International Journal of Structural Mechanicsand Finite Elements

5 more...4 more...

3 more...

Biotechnology « International Journal of Industrial Biotechnology and

Biomaterials« International Journal of Plant Biotechnology« International Journal of Molecular Biotechnology« International Journal of Biochemistry and Biomolecules« International Journal of Animal Biotechnology and

Applications3 more...

Nursing « International Journal of Immunological Nursing« International Journal of Cardiovascular Nursing« International Journal of Neurological Nursing« International Journal of Orthopedic Nursing« International Journal of Oncological Nursing

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International Journal of Cheminformatics - Vol 2_Issue 2

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