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Molecular Modelling and Simulations in Cancer Research

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Molecular Modelling and Simulations in Cancer Research Biochimica et Biophysica Acta 1836 (2013) 1–14 Contents lists available at SciVerse ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbacan Review Molecular modelling and simulations in cancer research Ran Friedman a,e,⁎, Kjetil Boye b,c, Kjersti Flatmark b,d a Computational Chemistry and Biochemistry Group, School of Natural Sciences, Linnæus University, 391 82 Kalmar, Sweden b Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway c Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway d Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway e Linnæus University, Biomaterials Chemistry Centre of Excellence, 391 82 Kalmar, Sweden article info abstract Article history: Thecomplexityofcancerandthevastamountofexperimentaldataavailablehavemadecomputer-aidedap- Received 10 December 2012 proaches necessary. Biomolecular modelling techniques are becoming increasingly easier to use, whereas hardware Received in revised form 4 February 2013 and software are becoming better and cheaper. Cross-talk between theoretical and experimental scientists dealing Accepted 5 February 2013 with cancer-research from a molecular approach, however, is still uncommon. This is in contrast to other fields, Available online 14 February 2013 such as amyloid-related diseases, where molecular modelling studies are widely acknowledged. The aim of this review paper is therefore to expose some of the more common approaches in molecular modelling to cancer Keywords: Molecular dynamics scientists in simple terms, illustrating success stories while also revealing the limitations of computational studies AKR1B10 at the molecular level. Tubulin polymerase © 2013 Elsevier B.V. All rights reserved. Pin1 ERK2 L-asparaginase p53 Contents 1. Introduction .............................................................. 2 2. Methods of molecular modelling and simulation .............................................. 2 2.1. Atomistic simulation and modelling methods ............................................ 3 2.1.1. Atomistic molecular dynamics simulations ......................................... 3 2.1.2. Brownian dynamics ................................................... 4 2.1.3. Modelling based on quantum chemistry .......................................... 4 2.1.4. Ab initio molecular dynamics ............................................... 4 2.1.5. Quantum mechanics/molecular mechanics ......................................... 5 2.1.6. Normal mode analysis .................................................. 5 2.2. Modelling of structures of proteins and protein complexes ..................................... 5 2.2.1. Homology modelling ................................................... 6 2.2.2. De-novo modelling of protein structures (fold recognition methods) ............................. 7 2.2.3. Modelling of protein complexes .............................................. 7 2.3. Protein–drug interaction prediction ................................................ 7 2.3.1. Docking of drug-like molecules into protein targets .................................... 7 2.4. Simplified models that can yield biological insights ......................................... 8 2.4.1. Elastic network models .................................................. 8 2.4.2. Coarse-grained simulations ................................................ 8 2.4.3. Dissipative particle dynamics ............................................... 8 Abbreviations: AIMD, ab initio molecular dynamics; AEP, asparagine endopeptidase; ALK, anaplastic lymphoma kinase; BD, Brownian dynamics; CPMD, Car–Parrinello molecular dynamics; DFT, density functional theory; DPD, dissipative particle dynamics; ENM, elastic network model; ERK2, extracellular signal-regulated kinase 2; EXAFS, extended X-ray absorption fine structure; FRET, Förster resonance energy transfer; L-ASN, L-asparaginase; MD, molecular dynamics; NMA, normal mode analysis; QM, quantum mechanics; QM/ MM, quantum mechanics/molecular mechanics; SAXS, small angle X-ray scattering; YAS, yttrium-alumino-silicate ⁎ Corresponding author at: Linnæus University, Biomaterials Chemistry Centre of Excellence, 391 82 Kalmar, Sweden. Tel.: +46 480446290. E-mail address: [email protected] (R. Friedman). 0304-419X/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.bbcan.2013.02.001 2 R. Friedman et al. / Biochimica et Biophysica Acta 1836 (2013) 1–14 3. Examples of modelling and simulation studies as relevant to cancer-research ................................ 8 3.1. The catalytic activity of the aldo-keto-reductase tumour marker AKR1B10 . ............................ 8 3.2. Understanding the mechanism of tubulin polymerisation inhibitors ................................. 9 3.3. Recognition of phosphorylated substrates by Pin1 .......................................... 9 3.4. Autoactivation of ERK2 ...................................................... 9 3.5. Engineering of a therapeutic protein ................................................ 9 3.6. Computational approach discriminates functional activity of p53 mutants . ............................ 9 3.7. Atomistic structures of yttrium-containing glasses for cancer therapy ................................. 9 4. Potentialapplicationsformolecularmodellingincancerresearch.......................................10 4.1. Prediction of functional consequences of molecular alterations ....................................10 4.2. Therapeutic aspects ........................................................10 5. Conclusions and outlook .........................................................10 Acknowledgement ..............................................................11 Appendix A. Computer programs and webservers ..............................................11 References ..................................................................1113 1. Introduction and medicine, this article provides added insights with respect to use of the molecular modelling techniques within cancer research. A large number of proteins have been shown to be involved in various types of cancer, from the ubiquitous tumour suppressor p53 2. Methods of molecular modelling and simulation to metastasis promoters such as S100A4. Accordingly, whereas drug design was once aimed primarily at the tumour level, many newer “Molecular modelling” has gone a long way since its early days. Most drugs are protein-specific. Such drugs often have less severe side of the readers are probably familiar with the plastic balls and sticks effects, because they selectively aim at proteins that are related to that connect them, which were used in chemistry classes to teach cancer progression. Moreover, owing to the availability of affordable how molecules are made from atoms. Such models had also been sequencing techniques and plethora of genetic markers, personalised used in research [10], but were replaced with computer-generated treatments are beginning to be available [1]. On the other hand, suffi- models. Today, “molecular modelling” refers to the application of cient knowledge about the biology of many cancer-related proteins computer-generated models in molecular studies ranging from a few and mutations is still missing. Very often, a marker of a certain cancer atoms to multitude of biomolecules. These models are used to simulate is identified but it is not clear how it is related to the specific disease. processes that may be as fast as 10−15 s or as slow as a few seconds. Many details on a given protein's function(s), and how it is altered Clearly, the accuracy and level of detail depend on the size and time- by different mutations, become clear once the protein's structure is scale of the system. Sub-Ångström differences between structures can known. Proteins, however, are not static and it is their dynamic land- be studied and have a large influence on the binding of a drug molecule scape that determines their roles [2]. Nuclear magnetic resonance to its receptor, whereas the size of protein complexes is three orders of (NMR), Förster resonance energy transfer (FRET), X-ray Laue diffrac- magnitude larger. These differences necessitate the use of different tion, extended X-ray absorption fine structure (EXAFS) and other bio- methods. In general, the more accurate the method at hand, the more physical methods can shed light on the dynamics of macromolecules, time and computational resources will be needed to get a meaningful but suffer from some limitations in terms of sensitivity, applicability, result (for systems of similar size). The choice of the modelling method and time scales. Computer-aided studies can complement molecular is therefore made based upon the problem at hand. studies and yield details that are not available to the experiment. Although it is possible to model a collection of molecules, such as Molecular modelling approaches therefore become increasingly use- multiple peptides and lipids [11], most molecular modelling studies ful in many clinically-oriented studies, e.g., amyloid related diseases related to cancer research are carried out in atomistic details. These [3]. Such methods, however, are sometimes inaccessible to the cancer methods, however, are limited in scope to molecules for which structur- researcher owing to lack of understanding on their potential use, al data are available from
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