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Hsu HH, Huang CH, Lin ST. New Data Structure for Computational Molecular Design with Atomic or Fragment Resolution. J Chem Inf Model 2019; 59:3703-3713. [PMID: 31393721 DOI: 10.1021/acs.jcim.9b00478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new molecular data structure and molecular structure operation algorithms are proposed for general purpose molecular design. The data structure allows for a variety of molecular operations for creating new molecules. Two types of molecular operations were developed, unimolecular and bimolecular operations. In unimolecular operations, a child molecule can be created from a parent via addition of a functional group, deletion of a fragment, mutation of an atom, etc. In bimolecular operations, children molecules are generated from two parent molecules through combination or crossover (hybridization). These molecular operations are essential for the creation and modification of molecules for the purpose of molecular design. The data structure is capable of representing linear, branched, multifunctional, and multivalent compounds. Algorithms are developed for deriving the molecular data structure of a molecule from its atomic coordinates and vice versa. We show that this new molecular data structure and the developed algorithms, referred to as Molecular Assembling and Representation Suite, allow one to generate a comprehensive library of new molecules via performing every possible molecular structure modification.
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Affiliation(s)
- Hsuan-Hao Hsu
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
| | - Chen-Hsuan Huang
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
| | - Shiang-Tai Lin
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
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Reymond JL, Ruddigkeit L, Blum L, van Deursen R. The enumeration of chemical space. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1104] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Tsai TY, Chang KW, Chen CYC. iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan. J Comput Aided Mol Des 2011; 25:525-31. [PMID: 21647737 DOI: 10.1007/s10822-011-9438-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/16/2011] [Indexed: 11/26/2022]
Abstract
The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.
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Affiliation(s)
- Tsung-Ying Tsai
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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Hartenfeller M, Schneider G. Enabling future drug discovery by
de novo
design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.49] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Markus Hartenfeller
- Computer‐Assisted Drug Design, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland
| | - Gisbert Schneider
- Computer‐Assisted Drug Design, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland
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Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 2005; 4:649-63. [PMID: 16056391 DOI: 10.1038/nrd1799] [Citation(s) in RCA: 536] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ever since the first automated de novo design techniques were conceived only 15 years ago, the computer-based design of hit and lead structure candidates has emerged as a complementary approach to high-throughput screening. Although many challenges remain, de novo design supports drug discovery projects by generating novel pharmaceutically active agents with desired properties in a cost- and time-efficient manner. In this review, we outline the various design concepts and highlight current developments in computer-based de novo design.
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Affiliation(s)
- Gisbert Schneider
- Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Marie-Curie-Str. 11 D-60439 Frankfurt am Main, Germany.
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Abstract
To accommodate situations in which the 3D structure of the target receptor is not available, we have developed the Pseudo Atomic Receptor Model (PARM) software package. In this article we describe PARM and illustrate its use with three examples: elemenes (potential anticancer drugs), angiotensin converting enzyme inhibitors, and human HIV-1 inhibitors TTD (1,1,3-trioxo-2H, 4H-thieno[3,4-e][1,2,4] thiadiazine derivatives). The results show that PARM can build models with favorable cross-validation statistics (Rcv2 values 0.7-0.9) and give helpful SAR insight. PARM has certain advantages: (a) it can be used for many systems, regardless of whether the 3D structure of the receptor is known; (b) PARM models were demonstrated to be highly statistically reliable; and (c) PARM analyses are robust and reproducible.
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Affiliation(s)
- J Pei
- Laboratory of Computer Chemistry (LCC), Institute of Chemical Metallurgy, Chinese Academy of Sciences, P.O. Box 353, 100080, Beijing, China
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Hindle SA, Rarey M, Buning C, Lengaue T. Flexible docking under pharmacophore type constraints. J Comput Aided Mol Des 2002; 16:129-49. [PMID: 12188022 DOI: 10.1023/a:1016399411208] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
FLEXX-PHARM, an extended version of the flexible docking tool FLEXX, allows the incorporation of information about important characteristics of protein-ligand binding modes into a docking calculation. This information is introduced as a simple set of constraints derived from receptor-based type pharmacophore features. The constraints are determined by selected FLEXX interactions and inclusion volumes in the receptor active site. They guide the docking process to produce a set of docking solutions with particular properties. By applying a series of look-ahead checks during the flexible construction of ligand fragments within the active site, FLEXX-PHARM determines which partially built docking solutions can potentially obey the constraints. Solutions that will not obey the constraints are deleted as early as possible, often decreasing the calculation time and enabling new docking solutions to emerge. FLEXX-PHARM was evaluated on various individual protein-ligand complexes where the top docking solutions generated by FLEXX had high root mean square deviations (RMSD) from the experimentally observed binding modes. FLEXX-PHARM showed an improvement in the RMSD of the top solutions in most cases, along with a reduction in run time. We also tested FLEXX-PHARM as a database screening tool on a small dataset of molecules for three target proteins. In two cases, FLEXX-PHARM missed one or two of the active molecules due to the constraints selected. However, in general FLEXX-PHARM maintained or improved the enrichment shown with FLEXX, while completing the screen in considerably less run time.
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Affiliation(s)
- Sally A Hindle
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany.
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Barone R, Barone R, Arbelot M, Chanon M. gasp: a computer program to generate automatically polycyclic structures. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00562-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Murray CW, Clark DE, Auton TR, Firth MA, Li J, Sykes RA, Waszkowycz B, Westhead DR, Young SC. PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology. J Comput Aided Mol Des 1997; 11:193-207. [PMID: 9089436 DOI: 10.1023/a:1008094712424] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This paper describes a novel methodology, PRO_SELECT, which combines elements of structure-based drug design and combinatorial chemistry to create a new paradigm for accelerated lead discovery. Starting with a synthetically accessible template positioned in the active site of the target of interest, PRO_SELECT employs database searching to generate lists of potential substituents for each substituent position on the template. These substituents are selected on the basis of their being able to couple to the template using known synthetic routes and their possession of the correct functionality to interact with specified residues in the active site. The lists of potential substituents are then screened computationally against the active site using rapid algorithms. An empirical scoring function, correlated to binding free energy, is used to rank the substituents at each position. The highest scoring substituents at each position can then be examined using a variety of techniques and a final selection is made. Combinatorial enumeration of the final lists generates a library of synthetically accessible molecules, which may then be prioritized for synthesis and assay. The results obtained using PRO_SELECT to design thrombin inhibitors are briefly discussed.
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Affiliation(s)
- C W Murray
- Proteus Molecular Design Ltd., Macclesfield, Cheshire, U.K
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Luo Z, Wang R, Lai L. RASSE: a new method for structure-based drug design. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1996; 36:1187-94. [PMID: 8941995 DOI: 10.1021/ci950277w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A novel method, RASSE, has been developed to suggest reasonable structures which can fit well to the binding sites of receptors. Molecules are generated by an iterative growing procedure in which atoms are added to existing fragments. Potential ligands are then picked out by special scoring rules. This atomgrowing based method is characterized by combinatorial searching of atom types and conformations. To some extent, it is the computer simulation of combinatorial chemistry. This method has been applied to the design of inhibitors for E. coli dihydrofolate reductase and human phospholipase A2. The results demonstrate that this program is capable of generating reasonable structures, thus proving its power in drug design.
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Affiliation(s)
- Z Luo
- Institute of Physical Chemistry, Peking University, Beijing, P.R. China
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Clark DE, Westhead DR, Sykes RA, Murray CW. Active-site-directed 3D database searching: pharmacophore extraction and validation of hits. J Comput Aided Mol Des 1996; 10:397-416. [PMID: 8951650 DOI: 10.1007/bf00124472] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two new computational tools, PRO_PHARMEX and PRO_SCOPE, for use in active-site-directed searching of 3D databases are described. PRO_PHARMEX is a flexible, graphics-based program facilitating the extraction of pharmacophores from the active site of a target macromolecule. These pharmacophores can then be used to search a variety of databases for novel lead compounds. Such searches can often generate many 'hits' of varying quality. To aid the user in setting priorities for purchase, synthesis or testing, PRO_SCOPE can be used to dock molecules rapidly back into the active site and to assign them a score using an empirical scoring function correlated to the free energy of binding. To illustrate how these tools can add value to existing 3D database software, their use in the design of novel thrombin inhibitors is described.
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Affiliation(s)
- D E Clark
- Proteus Molecular Design Ltd., Macclesfield, Cheshire, U.K
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