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Olotu FA, Munsamy G, Soliman MES. Does Size Really Matter? Probing the Efficacy of Structural Reduction in the Optimization of Bioderived Compounds - A Computational "Proof-of-Concept". Comput Struct Biotechnol J 2018; 16:573-586. [PMID: 30546858 PMCID: PMC6280605 DOI: 10.1016/j.csbj.2018.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 02/07/2023] Open
Abstract
Over the years, numerous synthetic approaches have been utilized in drug design to improve the pharmacological properties of naturally derived compounds and most importantly, minimize toxic effects associated with their transition to drugs. The reduction of complex bioderived compounds to simpler bioactive fragments has been identified as a viable strategy to develop lead compounds with improved activities and minimal toxicities. Although this ‘reductive’ strategy has been widely exemplified, underlying biological events remain unresolved, hence the unanswered question remains how does the fragmentation of a natural compound improve its bioactivity and reduce toxicities? Herein, using a combinatorial approach, we initialize a computational “proof-of- concept” to expound the differential pharmacological and antagonistic activities of a natural compound, Anguinomycin D, and its synthetic fragment, SB640 towards Exportin Chromosome Region Maintenance 1 (CRM1). Interestingly, our findings revealed that in comparison with the parent compound, SB640 exhibited improved pharmacological attributes, while toxicities and off-target activities were relatively minimal. Moreover, we observed that the reduced size of SB640 allowed ‘deep access’ at the Nuclear Export Signals (NES) binding groove of CRM1, which favored optimal and proximal positioning towards crucial residues while the presence of the long polyketide tail in Anguinomycin D constrained its burial at the hydrophobic groove. Furthermore, with regards to their antagonistic functions, structural inactivation (rigidity) was more pronounced in CRM1 when bound by SB640 as compared to Anguinomycin D. These findings provide essential insights that portray synthetic fragmentation of natural compounds as a feasible approach towards the discovery of potential leads in disease treatment.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Geraldene Munsamy
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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When fragments link: a bibliometric perspective on the development of fragment-based drug discovery. Drug Discov Today 2018; 23:1596-1609. [DOI: 10.1016/j.drudis.2018.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/02/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022]
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Combes RD, Balls M. Every silver lining has a cloud: the scientific and animal welfare issues surrounding a new approach to the production of transgenic animals. Altern Lab Anim 2014; 42:137-45. [PMID: 24901907 DOI: 10.1177/026119291404200206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The scientific basis and advantages of using recently developed CRISPR/Cas-9 technology for transgenesis have been assessed with respect to other production methods, laboratory animal welfare, and the scientific relevance of transgenic models of human diseases in general. As the new technology is straightforward, causes targeted DNA double strand breaks and can result in homozygous changes in a single step, it is more accurate and more efficient than other production methods and speeds up transgenesis. CRISPR/Cas-9 also obviates the use of embryonic stem cells, and is being used to generate transgenic non-human primates (NHPs). While the use of this method reduces the level of animal wastage resulting from the production of each new strain, any long-term contribution to reduction will be offset by the overall increase in the numbers of transgenic animals likely to result from its widespread usage. Likewise, the contribution to refinement of using a more-precise technique, thereby minimising the occurrence of unwanted genetic effects, will be countered by a probable substantial increase in the production of transgenic strains of increasingly sentient species. For ethical and welfare reasons, we believe that the generation of transgenic NHPs should be allowed only in extremely exceptional circumstances. In addition, we present information, which, on both welfare and scientific grounds, leads us to question the current policy of generating ever-more new transgenic models in light of the general failure of many of them, after over two decades of ubiquitous use, to result in significant advances in the understanding and treatment of many key human diseases. Because this unsatisfactory situation is likely to be due to inherent, as well as possibly avoidable, limitations in the transgenic approach to studying disease, which are briefly reviewed, it is concluded that a thorough reappraisal of the rationale for using genetically-altered animals in fundamental research and by the pharmaceutical industry, and for its support by funding bodies, should be undertaken. In the meantime, the use of CRISPR/Cas-9 to generate new transgenic cells in culture is to be guardedly encouraged.
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Grime KH, Barton P, McGinnity DF. Application of In Silico, In Vitro and Preclinical Pharmacokinetic Data for the Effective and Efficient Prediction of Human Pharmacokinetics. Mol Pharm 2013; 10:1191-206. [DOI: 10.1021/mp300476z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kenneth H. Grime
- Respiratory & Inflammation DMPK, AstraZeneca R&D, Mölndal, SE 43183 Mölndal, Sweden
| | - Patrick Barton
- Respiratory & Inflammation DMPK, AstraZeneca R&D, Mölndal, SE 43183 Mölndal, Sweden
| | - Dermot F. McGinnity
- Respiratory & Inflammation DMPK, AstraZeneca R&D, Mölndal, SE 43183 Mölndal, Sweden
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Lu Y. Integrating experimentation and quantitative modeling to enhance discovery of Beta amyloid lowering therapeutics for Alzheimer's disease. Front Pharmacol 2012; 3:177. [PMID: 23060797 PMCID: PMC3463859 DOI: 10.3389/fphar.2012.00177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 09/14/2012] [Indexed: 11/29/2022] Open
Abstract
Drug discovery can benefit from a proactive-knowledge-attainment philosophy which strategically integrates experimentation and pharmacokinetic/pharmacodynamic (PK/PD) modeling. Our programs for Alzheimer’s disease (AD) illustrate such an approach. Compounds that inhibit the generation of brain beta amyloid (Aβ), especially Aβ42, are being pursued as potential disease-modifying therapeutics. Complexities in the PK/Aβ relationship for these compounds have been observed and the data require an advanced approach for analysis. We established a semimechanistic PK/PD model that can describe the PK/Aβ data by accounting for Aβ generation and clearance. The modeling characterizes the in vivo PD (i.e., Aβ lowering) properties of compounds and generates insights about the salient biological systems. The learning from the modeling enables us to establish a framework for predicting in vivo Aβ lowering from in vitro parameters.
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Affiliation(s)
- Yasong Lu
- Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development Groton, CT, USA
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Leung EL, Cao ZW, Jiang ZH, Zhou H, Liu L. Network-based drug discovery by integrating systems biology and computational technologies. Brief Bioinform 2012; 14:491-505. [PMID: 22877768 PMCID: PMC3713711 DOI: 10.1093/bib/bbs043] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple '-omics' databases. The newly developed algorithm- or network-based computational models can tightly integrate '-omics' databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various '-omics' platforms and computational tools would accelerate development of network-based drug discovery and network medicine.
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Affiliation(s)
- Elaine L Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
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7
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Rethinking leadership in drug discovery projects. Drug Discov Today 2012; 17:1258-62. [PMID: 22706018 DOI: 10.1016/j.drudis.2012.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/25/2012] [Accepted: 06/07/2012] [Indexed: 11/23/2022]
Abstract
Great efforts have been dedicated to rebuilding the engine of pharmaceutical R&D. However, one potential area of improvement has received limited attention in the literature and in practice: namely, leadership. In this article, we enrich the traditional views of leadership, which consider leadership a responsibility of a few centrally placed authorities, with the concept of distributed leadership. Distributed leadership reflects a group-based capability driven by everyday activities and the key scientific questions at hand. We identify three leadership challenges faced by R&D teams that could be addressed by implementing distributed leadership. Furthermore, we provide some suggestions as to how to foster distributed leadership in drug discovery projects.
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Franci G, Miceli M, Altucci L. Targeting epigenetic networks with polypharmacology: a new avenue to tackle cancer. Epigenomics 2012; 2:731-42. [PMID: 22122079 DOI: 10.2217/epi.10.62] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The term 'epigenetic' fuses old and new concepts that refer to the modulation of gene expression in cellular heritability, fate, development and programming-reprogramming other than the DNA sequence itself. Epigenetic control of transcription is regulated by enzymes that mediate covalent modifications at gene-regulatory regions and histone proteins around which chromosomal DNA is wound. Many of the enzymes that mediate chromatin epigenetic reactions are deregulated in diseases such as cancer. Thus, small-molecule inhibitors that target chromatin-modifying enzymes represent a novel option for treatment, and DNA methyltransferase and histone deacetylase inhibitors have been approved for cancer treatment. Moreover, other classes of epi-enzymes (MS-275, SAHA) have been demonstrated to have strong disease association, and are currently being targeted for modulation. An epigenetic poly-pharmacological approach targeting multiple chromatin-modifying enzymes may represent a 'smart' option to treat cancer versus the current view on the selective and single pharmacological targeting of epigenetic enzymes.
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Sun C, Petros AM, Hajduk PJ. Fragment-based lead discovery: challenges and opportunities. J Comput Aided Mol Des 2011; 25:607-10. [DOI: 10.1007/s10822-011-9451-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 06/17/2011] [Indexed: 01/28/2023]
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Betz UA. Portfolio management in early stage drug discovery – a traveler's guide through uncharted territory. Drug Discov Today 2011; 16:609-18. [DOI: 10.1016/j.drudis.2011.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 03/09/2011] [Accepted: 04/27/2011] [Indexed: 11/30/2022]
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Abstract
Drug discovery must be guided not only by medical need and commercial potential, but also by the areas in which new science is creating therapeutic opportunities, such as target identification and the understanding of disease mechanisms. To systematically identify such areas of high scientific activity, we use bibliometrics and related data-mining methods to analyse over half a terabyte of data, including PubMed abstracts, literature citation data and patent filings. These analyses reveal trends in scientific activity related to disease studied at varying levels, down to individual genes and pathways, and provide methods to monitor areas in which scientific advances are likely to create new therapeutic opportunities.
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Affiliation(s)
- Pankaj Agarwal
- Computational Biology Department, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO BOX 1539, King of Prussia, Pennsylvania 19406, USA.
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Keighley W, Sewing A. New working paradigms in research laboratories. Drug Discov Today 2009; 14:625-9. [DOI: 10.1016/j.drudis.2009.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 05/01/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
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Targeting historically refractory interfaces: a partnership model that accelerates drug discovery within an expanded haystack. Future Med Chem 2009; 1:577-81. [PMID: 21426026 DOI: 10.4155/fmc.09.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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15
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Sirois S, Cloutier LM. Needed: system dynamics for the drug discovery process. Drug Discov Today 2008; 13:708-15. [DOI: 10.1016/j.drudis.2008.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 04/06/2008] [Accepted: 04/09/2008] [Indexed: 10/22/2022]
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17
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van Wyk AWW, Lobb KA, Caira MR, Hoppe HC, Davies-Coleman MT. Transformations of manool. tri- and tetracyclic norditerpenoids with in vitro activity against Plasmodium falciparum. JOURNAL OF NATURAL PRODUCTS 2007; 70:1253-8. [PMID: 17625894 DOI: 10.1021/np0701071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The known 17-norisopimar-15-ene-8beta,13beta-diol (5) and five new semisynthetic norditerpenoids, ethyl 17-norabiet-13(15)-E-en-8beta-ol-16-oate (6), ethyl 17-norabiet-13(15)-Z-en-8beta-ol-16-oate (7), 17-norpimaran-13alpha-ethoxy-8,16-olactone (8), 17-norisopimarane-8beta,15-diol (9), and 17-norarabiet-13(15)-ene-8beta,16-diol (10), were prepared from manool (11). Standard spectroscopic data including X-ray crystal analysis were used to determine the structures of 5-10. All five compounds exhibited in vitro antiplasmodial activity against the malarial parasite Plasmodium falciparum at varying microg mL(-1) concentrations.
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18
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Ator MA, Mallamo JP, Williams M. Overview of Drug Discovery and Development. ACTA ACUST UNITED AC 2006; Chapter 9:Unit9.9. [PMID: 22294181 DOI: 10.1002/0471141755.ph0909s35] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Sams-Dodd F. Drug discovery: selecting the optimal approach. Drug Discov Today 2006; 11:465-72. [PMID: 16635811 DOI: 10.1016/j.drudis.2006.03.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2005] [Revised: 03/06/2006] [Accepted: 03/21/2006] [Indexed: 10/24/2022]
Abstract
The target-based drug discovery approach has for the past 10-15 years been the dominating drug discovery paradigm. However, within the past few years, the commercial value of novel targets in licensing deals has fallen dramatically, reflecting that the probability of reaching a clinical drug candidate for a novel target is very low. This has naturally led to questions regarding the success of target-based drug discovery and, more importantly, a search for alternatives. This paper evaluates the strengths and limitations of the main drug discovery approaches, and proposes a novel approach that could offer advantages for the identification of disease-modifying treatments.
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Affiliation(s)
- Frank Sams-Dodd
- Bionomics Europe, Les Algorithmes, rue Jean Sapidus, Parc d'Innovation, 67400 Illkirch, France.
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Carney S. Question: what do you call 500 scientists coming together to address the productivity gap? Answer: a start. Drug Discov Today 2005; 10:1025-9. [PMID: 16055018 DOI: 10.1016/s1359-6446(05)03544-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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