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Sachdeo RA, Anthwal T, Nain S. Fragment based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2018-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Rational approaches towards drug development have emerged as one of the most promising ways among the tedious conventional procedures with the aim of redefining the drug discovery process. The need of current medical system is demanding a much precise, faster and reliable approaches in parallel to faster growing technology for development of drugs with more intrinsic action and fewer side effects. Systematic and well-defined diagnostic studies have revealed the specific causes of disease and related targets for drug development. Designing a drug as per the specific target, studying it in-silico prior to its development has been proved as an added benefit to the studies. Many approaches like structure based drug design, fragment based drug design and ligand based drug design are been in practice for the drug discovery and development with the similar fundamental theory. Fragment based drug design utilizes a library of fragments designed specifically for the concerned target and these fragments are studied further before screening with virtual methods as well as with biophysical methods. The process follows a well-defined pathway which moulds a fragment into a perfect drug candidate. In this chapter we have tried to cover all the basic aspects of fragment based drug design and related technologies.
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Affiliation(s)
- Rahul Ashok Sachdeo
- Department of Pharmaceutical Chemistry , Government College of Pharmacy , Karad , Maharashtra , 415124 , India
| | - Tulika Anthwal
- Department of Pharmacy , Banasthali Vidyapith , Banasthali , Rajasthan , 304022 , India
| | - Sumitra Nain
- Department of Pharmacy , Banasthali Vidyapith , Banasthali , Rajasthan , 304022 , India
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Yao L, Mustafa N, Tan EC, Poulsen A, Singh P, Duong-Thi MD, Lee JXT, Ramanujulu PM, Chng WJ, Yen JJY, Ohlson S, Dymock BW. Design and Synthesis of Ligand Efficient Dual Inhibitors of Janus Kinase (JAK) and Histone Deacetylase (HDAC) Based on Ruxolitinib and Vorinostat. J Med Chem 2017; 60:8336-8357. [DOI: 10.1021/acs.jmedchem.7b00678] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Lianbin Yao
- Department
of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Nurulhuda Mustafa
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 10, 117549, Singapore
| | - Eng Chong Tan
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Taiwan
International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, 115, Taiwan
| | - Anders Poulsen
- Experimental Therapeutics Centre, 31 Biopolis Way, 03-01 Nanos, 138669, Singapore
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Prachi Singh
- School
of Biological Sciences, Nanyang Technological University (NTU), 637551, Singapore
| | - Minh-Dao Duong-Thi
- School
of Biological Sciences, Nanyang Technological University (NTU), 637551, Singapore
| | - Jeannie X. T. Lee
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 10, 117549, Singapore
| | - Pondy Murugappan Ramanujulu
- Department
of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543, Singapore
- Centre
for Life Sciences Level 5, Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Wee Joo Chng
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 10, 117549, Singapore
- Cancer
Science Institute, National University of Singapore, 117599, Singapore
- National University Cancer Institute of Singapore, National University Health System, 119074, Singapore
| | - Jeffrey J. Y. Yen
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Sten Ohlson
- School
of Biological Sciences, Nanyang Technological University (NTU), 637551, Singapore
| | - Brian W. Dymock
- Department
of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543, Singapore
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Hage DS. Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications. Clin Chem 2017; 63:1083-1093. [PMID: 28396561 DOI: 10.1373/clinchem.2016.262253] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/02/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically related binding agent, are 2 methods that can be used to study these interactions. CONTENT This review presents various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. SUMMARY The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples.
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Affiliation(s)
- David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE.
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Singh P, Madhaiyan K, Duong-Thi MD, Dymock BW, Ohlson S. Analysis of Protein Target Interactions of Synthetic Mixtures by Affinity-LC/MS. SLAS DISCOVERY 2017; 22:440-446. [PMID: 28328315 DOI: 10.1177/2472555216687964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Analysis of interactions between molecules is of fundamental importance in life science research. In this study, we applied weak affinity chromatography, based on high-performance liquid chromatography and mass spectrometry, as a powerful tool for direct analysis of the components of a chemical reaction mixture for their binding to a target protein. As a demonstration of the potential of this method, we analyzed the binding of the compounds of the reaction mixture to the chaperone heat shock protein 90 (Hsp90). It was possible to analyze quantitatively the binding of the components of the mixture to the target independently from each other without any preceding process such as purification. This feature has wide implications in biological sciences as crude mixtures, either natural or synthetic, can be analyzed directly for their possible binding to a target. This method could lead to savings in costs and labor through shortening chemical research project development time.
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Affiliation(s)
- Prachi Singh
- 1 School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | | | - Minh-Dao Duong-Thi
- 1 School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Brian W Dymock
- 2 Department of Pharmacy, National University of Singapore (NUS), Singapore
| | - Sten Ohlson
- 1 School of Biological Sciences, Nanyang Technological University (NTU), Singapore
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