51
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Follow-on drugs: How far should chemists look? Drug Discov Today 2011; 16:722-32. [DOI: 10.1016/j.drudis.2011.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 04/08/2011] [Accepted: 05/20/2011] [Indexed: 01/27/2023]
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52
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Abstract
Applying similarity for finding new promising compounds is a key issue in drug design. Conversely, quantifying similarity between molecules has remained a difficult task despite the numerous approaches. Here, some general aspects along with recent developments regarding similarity criteria are collected. For the purpose of virtual screening, the compounds have to be encoded into a computer-readable format that permits a comparison, according to given similarity criteria, comprising the use of the 3D structure, fingerprints, graph-based and alignment-based approaches. Whereas finding the most common substructures is the most obvious method, more recent approaches take into account chemical modifications that appear throughout existing drugs, from various therapeutic categories and targets.
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53
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54
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Warr WA. Guiding effective decisions: an interview with Matthew Segall, CEO of Optibrium. J Comput Aided Mol Des 2011; 25:103-6. [DOI: 10.1007/s10822-011-9411-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 01/02/2011] [Indexed: 11/24/2022]
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55
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Clark AM. Basic primitives for molecular diagram sketching. J Cheminform 2010; 2:8. [PMID: 20923555 PMCID: PMC2958898 DOI: 10.1186/1758-2946-2-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/05/2010] [Indexed: 11/22/2022] Open
Abstract
A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates for molecular structures using a bare minimum of input bandwidth. The input requirements for each primitive consist of a small number of discrete choices, which means that these primitives can be used to form the basis of a user interface which does not require an accurate pointing device. This is particularly relevant to software designed for contemporary mobile platforms. The reduction of input bandwidth is accomplished by using algorithmic methods for anticipating probable geometries during the sketching process, and by intelligent use of template grafting. The algorithms and their uses are described in detail.
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Affiliation(s)
- Alex M Clark
- Molecular Materials Informatics, Inc, Montréal, QC, Canada.
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56
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Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation. Drug Discov Today 2010; 15:804-11. [PMID: 20727982 DOI: 10.1016/j.drudis.2010.08.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 07/08/2010] [Accepted: 08/11/2010] [Indexed: 01/08/2023]
Abstract
We propose a numerical framework that permits an effective atlas-like representation of chemico-biological space based on a series of Cartesian planes mapping the ligands with the corresponding targets connected by an affinity parameter (K(i) or related). The numerical framework is derived from the concept of ligand efficiency indices, which provide a natural coordinate system combining the potency toward the target (biological space) with the physicochemical properties of the ligand (chemical space). This framework facilitates navigation in the multidimensional drug discovery space using map-like representations based on pairs of combined variables related to the efficiency of the ligands per Dalton (molecular weight or number of non-hydrogen atoms) and per unit of polar surface area (or number of polar atoms).
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57
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Warner DJ, Griffen EJ, St-Gallay SA. WizePairZ: A Novel Algorithm to Identify, Encode, and Exploit Matched Molecular Pairs with Unspecified Cores in Medicinal Chemistry. J Chem Inf Model 2010; 50:1350-7. [DOI: 10.1021/ci100084s] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel J. Warner
- Department of Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom, and Cancer and Infection Research, AstraZeneca R&D Alderley, Alderley Park, Macclesfield, Cheshire. SK10 4TG, United Kingdom
| | - Edward J. Griffen
- Department of Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom, and Cancer and Infection Research, AstraZeneca R&D Alderley, Alderley Park, Macclesfield, Cheshire. SK10 4TG, United Kingdom
| | - Stephen A. St-Gallay
- Department of Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom, and Cancer and Infection Research, AstraZeneca R&D Alderley, Alderley Park, Macclesfield, Cheshire. SK10 4TG, United Kingdom
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58
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Ekins S, Gupta RR, Gifford E, Bunin BA, Waller CL. Chemical space: missing pieces in cheminformatics. Pharm Res 2010; 27:2035-9. [PMID: 20683645 DOI: 10.1007/s11095-010-0229-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/23/2010] [Indexed: 11/29/2022]
Abstract
Cheminformatics is at a turning point, the pharmaceutical industry benefits from using the various methods developed over the last twenty years, but in our opinion we need to see greater development of novel approaches that non-experts can use. This will be achieved by more collaborations between software companies, academics and the evolving pharmaceutical industry. We suggest that cheminformatics should also be looking to other industries that use high performance computing technologies for inspiration. We describe the needs and opportunities which may benefit from the development of open cheminformatics technologies, mobile computing, the movement of software to the cloud and precompetitive initiatives.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 601 Runnymede Avenue, Jenkintown, Pennsylvania 19046, USA.
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59
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Cucurull-Sanchez L. Successful identification of key chemical structure modifications that lead to improved ADME profiles. J Comput Aided Mol Des 2010; 24:449-58. [DOI: 10.1007/s10822-010-9361-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 04/26/2010] [Indexed: 11/28/2022]
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60
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Muchmore SW, Edmunds JJ, Stewart KD, Hajduk PJ. Cheminformatic Tools for Medicinal Chemists. J Med Chem 2010; 53:4830-41. [DOI: 10.1021/jm100164z] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Steven W. Muchmore
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064
| | - Jeremy J. Edmunds
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064
| | - Kent D. Stewart
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064
| | - Philip J. Hajduk
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064
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61
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Herman Skolnik award symposium honoring Yvonne Martin. J Comput Aided Mol Des 2009; 23:831-6. [DOI: 10.1007/s10822-009-9310-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 11/17/2009] [Indexed: 11/25/2022]
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62
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Raymond JW, Watson IA, Mahoui A. Rationalizing Lead Optimization by Associating Quantitative Relevance with Molecular Structure Modification. J Chem Inf Model 2009; 49:1952-62. [DOI: 10.1021/ci9000426] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John W. Raymond
- Discovery Informatics and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Ian A. Watson
- Discovery Informatics and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Abdelaziz Mahoui
- Discovery Informatics and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
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63
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Jordan AM, Roughley SD. Drug discovery chemistry: a primer for the non-specialist. Drug Discov Today 2009; 14:731-44. [PMID: 19416759 DOI: 10.1016/j.drudis.2009.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 02/20/2009] [Accepted: 04/23/2009] [Indexed: 11/25/2022]
Abstract
Like all scientific disciplines, drug discovery chemistry is rife with terminology and methodology that can seem intractable to those outside the sphere of synthetic chemistry. Derived from a successful in-house workshop, this Foundation Review aims to demystify some of this inherent terminology, providing the non-specialist with a general insight into the nomenclature, terminology and workflow of medicinal chemists within the pharmaceutical industry.
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Affiliation(s)
- Allan M Jordan
- Medicinal Chemistry, Vernalis (R&D) Ltd., Granta Park, Cambridge CB21 6GB, UK.
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64
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Krier M, Hutter MC. Bioisosteric Similarity of Molecules Based on Structural Alignment and Observed Chemical Replacements in Drugs. J Chem Inf Model 2009; 49:1280-97. [DOI: 10.1021/ci8003418] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Markus Krier
- Center for Bioinformatics, Saarland University, Campus Building C7.1, D-66123 Saarbruecken, Germany
| | - Michael C. Hutter
- Center for Bioinformatics, Saarland University, Campus Building C7.1, D-66123 Saarbruecken, Germany
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65
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Taft CA, Da Silva VB, Da Silva CHTDP. Current topics in computer-aided drug design. J Pharm Sci 2008; 97:1089-98. [PMID: 18214973 DOI: 10.1002/jps.21293] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The addition of computer-aided drug design (CADD) technologies to the research and drug discovery approaches could lead to a reduction of up to 50% in the cost of drug design. Designing a drug is the process of finding or creating a molecule which has a specific activity on a biological organism. Development and drug discovery is a time-consuming, expensive, and interdisciplinary process whereas scientific advancements during the past two decades have altered the way pharmaceutical research produces new bioactive molecules. Advances in computational techniques and hardware solutions have enabled in silico methods to speed up lead optimization and identification. We will review current topics in computer-aided molecular design underscoring some of the most recent approaches and interdisciplinary processes. We will discuss some of the most efficient pathways and design.
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Affiliation(s)
- Carlton A Taft
- Centro Brasileiro de Pesquisas Físicas, Rua Dr. Xavier Sigaud, 150, Urca, 22290-180 Rio de Janeiro, Brazil.
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66
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Hajduk PJ, Sauer DR. Statistical analysis of the effects of common chemical substituents on ligand potency. J Med Chem 2008; 51:553-64. [PMID: 18173228 DOI: 10.1021/jm070838y] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The results of a statistical analysis of more than 84,000 compounds from lead optimization programs against 30 different protein targets is presented, with a focus on the effects that different chemical substituents have on compound potency. It is observed that the potency changes induced by most chemical groups follows a nearly normal distribution centered near zero (i.e., no effect on potency). However, the widths of the distributions vary significantly between different substituents, and these effects cannot be rationalized by simple physicochemical parameters. In addition, certain substituents consistently bias the distribution toward higher or lower potency, suggesting the existence of preferred and nonpreferred chemical groups for lead optimization. The implications of these results for understanding protein-ligand recognition and for enhancing the efficiency and speed of lead optimization will be discussed.
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Affiliation(s)
- Philip J Hajduk
- Pharmaceutical Discovery Division, GPRD, Abbott Laboratories, Abbott Park, IL 60064-6098, USA.
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67
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68
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Ensemble of hybrid neural network learning approaches for designing pharmaceutical drugs. Neural Comput Appl 2007. [DOI: 10.1007/s00521-007-0090-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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