International Journal of Cheminformatics Research vol 2 issue 2 by JournalsPub

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20 mit icle b rt u S A Applied Mechanics r International Journal of Electro Mechanics and u Mechanical Behaviour International Journal of Machine Design and Yo Manufacturing

Mechanical Engineering

¬ International Journal of Thermal Energy and

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

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Applications

International Journal of Mechanical Dynamics and Analysis International Journal of Fracture and damage Mechanics International Journal of Structural Mechanics and Finite Elements

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Materials Processing ¬ International Journal of Mechanical Handling and

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Electronics and Telecommunication « 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

Chemical Engineering « International Journal of Renewable Energy and its

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

Jul–Dec 2016

Civil Engineering

Planning « International Journal of Architecture and Infrastructure

Planning « International Journal of Rural and Regional Planning

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Development

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

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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 5 more...

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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 Energetic Materials International Journal of Bionics and Bio-Materials International Journal of Ceramics and Ceramic Technology International Journal of Bio-Materials and Biomedical Engineering 4 more...

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International Journal of Photochemistry International Journal of Analytical and Applied Chemistry International Journal of Green Chemistry International Journal of Chemical and Molecular Engineering 3 more...

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Biotechnology « International Journal of Industrial Biotechnology and « « « «

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Architecture « International Journal of Housing and Human Settlement

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Cheminformatics Research

Pollution

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Signals

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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 3 more... Applications

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

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International Journal of Cheminformatics Research 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

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PUBLICATION MANAGEMENT TEAM

Chairman Mr. Puneet Mehrotra Managing Director, JournalsPub, New Delhi

INTERNAL MEMBERS

Associate Manager Hidam Renubala

Commissioning Editors Ankita Singh

Dr. Chhavi Goel

Deepika Bhadauria

Manisha Dhoble Rekha Rani

EDITORIAL BOARD MEMBERS Dr. Yogesh Kumar Sharma Swami Shraddhanand College, Department of Chemistry, University of Delhi, New Delhi, India

Dr. Monika Gupta Department of Chemistry, University of Jammu, Jammu, India

Dr. P. V. Singh Department of Chemistry, Institute of Technology & Management, Uttar Pradesh, India

Dr. Sandeep Rai Department of Chemistry/Polymer and Rubber, Shroff S.R. Rotary Institute of Chemical Technology, Gujarat, India

Dr. Kishore Dasari Navin Fluorine International Limited, India

Dr. Kaman Singh Department of Chemistry (DST-FIST-PURSE Sponsored) Centre of Excellence (U.P. Govt., UGC-DRS (I) â&#x20AC;&#x201C;SAP Sponsored Department) Faculty of Science, University of Lucknow, Lucknow, India

Dr. Ajit Manharlal Bhavsar Dishman Pharmaceuticals and Chemicals Limited, Ahmedabad, India

Dr. Satyabrata Mohapatra Emami Limited, India

Dr. Susarla Venkata Ananta Rama Sastry MVGR 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

Contents 1. Structure-Based Drug Design for Therapeutic Application Aruna Singh

2. A Short Note on: Computer-Aided Molecular Design Zeanut Akoijam

3. Understanding Chemical Database Tools: A Guide to Beginners Amit Agnihotri

4. Brief Introduction to Cheminformatics Dayananda Singh Konjengbam

5. Developmental Process of New Medicines: A Brief Insight Varun Singh Parmar

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 ligandbased 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 structurebased 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

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International Journal of Cheminformatics Research 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 computeraided 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 commercially available.

are

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

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International Journal of Cheminformatics Research 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

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International Journal of Cheminformatics Research 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, information technology

ChemDraw,

computational

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,

science,

drug

discovery,

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

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International Journal of Cheminformatics Research 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, timeconsuming 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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Office No-4, 1 Floor, CSC, Pocket-E, Mayur Vihar, Phase-2, New Delhi-110091, India E-mail: info@journalspub.com

20 mit icle b rt u S A Applied Mechanics r International Journal of Electro Mechanics and u Mechanical Behaviour International Journal of Machine Design and Yo Manufacturing

Mechanical Engineering

¬ International Journal of Thermal Energy and

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

« « «

Applications

International Journal of Mechanical Dynamics and Analysis International Journal of Fracture and damage Mechanics International Journal of Structural Mechanics and Finite Elements

and Design ¬ International Journal of Manufacturing and

Materials Processing ¬ International Journal of Mechanical Handling and

Automation 5 more...

Electronics and Telecommunication « 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

Chemical Engineering « International Journal of Renewable Energy and its

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

Jul–Dec 2016

Civil Engineering

Planning « International Journal of Architecture and Infrastructure

Planning « International Journal of Rural and Regional Planning

« « « «

Development

« International Journal of Town Planning and Management

2 more...

Electrical Engineering

« « « «

Nursing

Material Sciences and Engineering

« « « «

5 more...

Biotechnology « International Journal of Industrial Biotechnology and « « « «

IJCR

1 more...

Architecture « International Journal of Housing and Human Settlement

« « « « «

Cheminformatics Research

Pollution

5 more...

Signals

« « « « «

International Journal of

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

Chemistry

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