Computational Prediction of Binding Affinity between Psychotropic Drugs and Neural Cytoskeleton Elements
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Computational Prediction of Binding Affinity between Psychotropic Drugs and Neural Cytoskeleton Elements The researchers used molecular dynamics simulations and docking to study the binding of cocaine, heroin, and LSD to microtubules and tubulin. They found that cocaine and heroin bound similarly to tubulin, but cocaine penetrated microtubules more deeply. LSD assumed a different position in both structures compared to the other drugs. The control drug taxol bound differently than the psychoactive substances. The study suggests microtubules may play an active role in binding psychotropic drugs and consciousness.
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Computational Prediction of Binding Affinity between Psychotropic Drugs and Neural Cytoskeleton Elements
- 1. Computational Prediction of Binding Affinity between Psychotropic Drugs and Neural Cytoskeleton Elements R. PIZZI1, T. RUTIGLIANO1, A. FERRAROTTI 2 and M. PREGNOLATO2 1Computer Science Department, University of Milan 2Department of Drug Sciences, University of Pavia
- 2. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 • Tubulin is a globular protein and the fundamental component of microtubules. • It is composed by two similar units, alpha and beta tubulin, bound very tightly together • . INTRO
- 3. INTRO • Microtubules are cylindrical polymers composed by aligned tubulin dimers, alpha and beta- tubulins, that polymerize in a helix that creates the microtubule.
- 4. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 • Microtubules (MTs) constitute the cytoskeleton of all the eukaryotic cells and are supposed to be involved in many key cellular functions. • MTs are claimed to possess peculiar functional properties that are under study. INTRO
- 5. Properties of microtubules • In the last decades many studies have been carried out that claim peculiar MTs quantum properties • Some hints and many theories seem to suggest that MTs may be involved in the consciuosness process. • Sir Roger Penrose, one of the major physicists of our age, maintains that inside MTs quantum superposition is sustained at room temperature, allowing a quantum computation that gives rise to consciousness. • Many scientists (e.g. Hameroff, Tuszinsky) support this or other similar theories.
- 6. Properties of microtubules • The present research follows other studies of our group that with direct in-vitro experiments and structural bioinformatics simulations have shown peculiar behavior of MTs • By means of specific physical measures of resonance and birefringence, that we also replicated in silico, we assessed a structural sensitivity of MTs in presence of electromagnetic field.
- 7. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 INTRO Project background tubulin, despite its symmetric structure, seems to have different internal forces that tend to resist a dynamic stabilization. However, in presence of electric field, although it tends to squash, it does not show any particular reaction. MTs react sharply to electromagnetic fields both in the experimental tests and in the simulations, showing to move and orient themselves along the field. The different behavior between microtubules and tubulin suggests that the tubular antenna-like shape of MTs is responsible of their peculiar properties
- 8. INTRO 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 - Our previous researches show that the peculiar properties of MTs could be due to their biological structure. - The present research aims to investigate with structural bioinformatics simulations the different behavior of tubulin and MTs in presence of consciousness-altering drugs - We meant to search for hints of a biological functional relationship between MTs and consciousness.
- 9. A deeper study of psychoactive drugs and their binding to tubulin and MTs structures may help us to better understand interactions and mechanisms. We examined: - A depressant drug (heroin) - A stimulant drug (cocaine) - A hallucinogen drug (LSD) INTRO Our aim 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Psychoactive drugs. Courtesy of Derek Snider.
- 10. INTRO Our aim 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Psychoactive drugs. Courtesy of Derek Snider.
- 11. To explore differences in binding with psychoactive drugs we performed: 1. Molecular Dynamics (MD) to carry out conformation optimization in water medium of cocaine, heroin, LSD 2. Docking procedures between structures (MTs and tubulin) and above mentioned drugs 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 INTRO Our aim
- 12. Material and Methods I step: MD Molecular Dynamics (MD): • Configurations are generated by application of the Newton equations of motion to all atoms simultaneously over a small time step to determine the new atomic positions and velocities • The force field is formed by the sum of molecular bonds and electrostatic forces • The total energy determines the evolution of this dynamical systems 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 13. MD: We used the Ascalaph Designer software This software combines Molecular Dynamics simulation in liquid phase (with explicit water molecules) with a graphical interface Material and Methods I step: MD 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 14. MD: Ascalaph Designer • flexible tool with many possible parameterizations for the force fields • various dynamical optimization techniques • graphical interface with many interactive methods for the development of molecular models • quantum computation • ab initio computational chemistry Material and Methods I step: MD 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 15. M D on ligands (psychoactive drugs): 1. The construction of the chemical structures was performed using the Ascalaph Designer ab-initio Free Drawing 2. The next step was the optimization, i.e. the energy minimization, of all the built chemical structures (energy minimization algorithm: conjugate gradient method, stop conditions: gradient value = 0.001 and iteration number = 100) Material and Methods I step: MD 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 16. • Most biological functions are mediated by interactions between proteins and ligands • The bond with a ligand can induce a conformational change that influences the activity or accessibility of other binding domains • We studied interactions between MTs, tubulin and drugs using HEX Protein Docking, a molecular docking software that allows both calculation and 3D visualization Source: http://hex.loria.fr/ Material and Methods II step: docking 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 17. • Docking algorithm: • The algorithm determines the geometric and electrostatic complementarity between two molecular structures • It projects the molecule in a 3D grid, performing a distinction between surface and interior atoms. Then it evaluates the overlapping degree of the molecular penetration relative to all the possible orientations of the molecule ligand around the macromolecolar structure. Material and Methods II step: docking 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 18. • HEX algorithm: it uses an FFT evolution called SPF (Spherical Polar Fourier): Each molecule is modelled in three dimensions using parametric functions that encode both the surface spatial potential distribution and their spherical polar coordinates Material and Methods II step: docking 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 The procedure searches for the best docking solution on the basis of a rigid 6-dimensional search on a rotational grid.
- 19. HEX Clustering Docking Results • It uses a clustering algorithm to group spatially similar docking orientations: • Each docking solution is first ordered by energy, and the lowest energy solution is considered the seed orientation for the first cluster. • Then the list of possible orientation is ordered on the basis of the intermolecular RMS distance between alpha-carbon chains • The process is repeated starting from the next lowest unassigned orientation, until all solutions have been assigned to a cluster. Material and methods Docking tool 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 20. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Material and Methods models TUBULIN (PDB 1JFF) MICROTUBULES (NANO-D research group at INRIA Grenoble-Rhone-Alpes )
- 21. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Material and Methods models LIGANDS: cocaine LSD heroin
- 22. • As control ligand we used taxol, a toxic substance that increases microtubule polymerization by binding to the filament and stabilizing it. • Taxol lacks in psychotropic characteristics, and is typically associated with Tubulin in the databanks • Ligands (cocaine, LSD , heroin, taxol) were subjected to docking using HEX. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Results
- 23. Results Taxol in tubulin Taxol in MT Taxol positions:
- 24. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Results C.LSD ligand in MTs A.Cocaine ligand in MTs B.Heroin ligand in MTs Alpha helix Beta sheet MTs
- 25. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Results Alpha helix Beta sheet • MT the two ligands heroin e cocaine are close to a kind of niche (perhaps the access way). • cocaine, compared to heroin, seems to penetrate further into the structure •heroin assumes a more superficial position, moving in the direction of an alpha helix.
- 26. 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Results Alpha helix Beta sheet •heroin and cocain are positioned both at Chain A. •The third ligand, LSD, shows a completely different position with respect to the other two ligands •LSD assumes a superficial position in contact with the two Chains and an alpha helix
- 27. Results C.LSD ligand in Tubulin B.Heroin ligand in Tubulin A.Cocaine ligand in Tubulin 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Alpha helix Beta sheet Tubulin
- 28. Results 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014 Alpha helix Beta sheet Results •cocaine and heroin show similar behavior: •they don’t appear to come in contact with any secondary structure, •they are present in a niche and positioned between chain A and B. •LSD takes a position similar to the other ligands, •LSD it is even more superficial and is only present at the level of one chain. Different observations have been made for tubulin:
- 29. Conclusions • We conclude that cocaine and heroin have similar localization in the tubulin structure, but not identical localization in MTs • LSD, however, assumes a completely different position compared to other ligands in both tubulin and in MT structures • The difference of the LSD behavior is evident in MT structure. • The control structure, Taxol, has a position completely different from the psychoactive substances, both in MT and in tubulin, suggesting that psychoactive substances have a different and specific role 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 30. Conclusions • As already amply demonstrated in our previous works, the MT tubular structure shows to have an important functional role that cannot be found in the only tubulin structure. • Mainstream science is used to consider other structures as targets for psychotrope substances • In our study MTs show to bind the drugs more deeply than tubulin • It can be hypothesized that MT are not just storage proteins but play an active role in the binding of the psychotrope drugs
- 31. Conclusions • In the future we aim to widen the study with other similar substances • If their binding sites should reveal to be similar to those found for heroin, cocain, LSD, our hypothesis of an active role of MTs in the cosciousness process. • Studies on complete sets of MTs with many copies of ligands could be realized by adopting in the future powerful PC clusters or a Supercomputer facility.
- 32. • A deeper study of consciousness-altering drugs and their binding to tubulin and MTs may help us to understand the complex biological interface between conscious and unconscious state • The worldwide research on the functional role of MTs is indeed still open and evolving. Conclusions 8th International Conference on APPLIED MATHEMATICS, SIMULATION, MODELLING. Florence, 2014
- 33. References • R. Pizzi , S. Fiorentini , G. Strini , M. Pregnolato, Exploring structural and dynamical properties of Microtubules by means of artificial neural networks. In: Complexity Science, Living Systems and Reflexing Interfaces: New Models and Perspectives, IGI Global New York, 2012, pp. 78-91 • R. Pizzi , G. Strini , S. Fiorentini, V. Pappalardo and M. Pregnolato, Evidences of new biophysical properties of Microtubules, In: Focus on artificial neural networks, Nova Science, 2010, pp. 191-207. • R. Pizzi , S. Fiorentini (2009). Artificial Neural Networks Identify the Dynamic Organization of Microtubules and Tubulin Subjected to Electromagnetic Field. In: Recent Advances in Applied Computer Science. Genova, 17-19 Oct 2009, p. 103-106, ISBN: 978-960-474- 127-4
Editor's Notes
- Each subunit of the microtubule is made of two slightly different but closely related simpler units calledalpha-tubulin and beta-tubulin that are bound very tightly together to form heterodimers In a microtubule, the subunits are organized in such a way that they all point the same direction to form 13 parallel protofilaments. This organization gives the structure polarity, with only the alpha-tubulin proteins exposed at one end and only beta-tubulin proteins at the other. By adding or removing globular tubulin proteins, the length of polymeric microtubules can be increased or decreased. Because the two ends of a microtubule are not the same, however, the rate at which growth or depolymerization occurs at each pole is different. The end of a polarized filament that grows and shrinks the fastest is known as the plus end and the opposing end is called the minus end. For all microtubules, the minus end is the one with exposed alpha-tubulins. In an animal cell, it is this end that is located at the centriole-containing centrosome found near the nucleus, while the plus end, comprised of exposedbeta-units, is projected out toward the cell's surface. Microtubules are continuously being assembled and disassembled so that tubulin monomers can be transported elsewhere to build microtubules when needed
- Each subunit of the microtubule is made of two slightly different but closely related simpler units calledalpha-tubulin and beta-tubulin that are bound very tightly together to form heterodimers In a microtubule, the subunits are organized in such a way that they all point the same direction to form 13 parallel protofilaments. This organization gives the structure polarity, with only the alpha-tubulin proteins exposed at one end and only beta-tubulin proteins at the other. By adding or removing globular tubulin proteins, the length of polymeric microtubules can be increased or decreased. Because the two ends of a microtubule are not the same, however, the rate at which growth or depolymerization occurs at each pole is different. The end of a polarized filament that grows and shrinks the fastest is known as the plus end and the opposing end is called the minus end. For all microtubules, the minus end is the one with exposed alpha-tubulins. In an animal cell, it is this end that is located at the centriole-containing centrosome found near the nucleus, while the plus end, comprised of exposedbeta-units, is projected out toward the cell's surface. Microtubules are continuously being assembled and disassembled so that tubulin monomers can be transported elsewhere to build microtubules when needed
- Project background: resonance and birefringence experiments Pizzi et al. [Pizzi, submitted] evaluated some biophysical properties of MTs by means of specific physical measures of resonance and birefringence to assess the structural sensitivity of microtubules in presence of electromagnetic field. The experimental results highlighted a physical behaviour of MTs in comparison with tubulin: MTs react in a different way compared to tubulin. The dynamic simulation of MT and tubulin subjected to electromagnetic field was performed via Molecular Dynamics (MD) tools. The tubulin, despite its symmetric structure, seems to have different internal forces that tend to resist a dynamic stabilization. However, in the presence of electric field, although it tends to squash, it does not show any particular reaction. Instead, microtubules react sharply to electromagnetic fields both in the experimental tests and in the simulations. The different behavior between microtubules and tubulin suggests that the tubular shape of microtubules is responsible of their peculiar properties, as in the case of carbon nanotubes (CNTs), that have same size and shape of microtubules and exhibit analogous (quantum) properties due to their antenna-like spatial structure: recent observations and experiments on CNTs have led to the development of an array of CNTs able to act as antennas [Wang, 2004]. These, instead to transmit and receive radio waves (measured in meters), due to their scale capture wavelengths at the nanoscale (measured in nanometers).
- A deeper study of consciousness-altering drugs and their binding to Tubulin and Microtubules may help us to better understand the complex biological interface between conscious and unconscious states and the various forms of psychopathology in a deeper physical framework. We are interested in evaluating the existence of any correlation between alterations of conscious states and molecular interactions within the cell. A number of drugs are able to bind to Tubulin and modify its activation state [2][3]. In particular, we are interested in studying as Heroin, Cocaine and LSD, chosen as most representative among depressive, exciting and hallucinogen drugs, respectively, affect Central Nervous System (CNS) and the conscious state understand the implications of hallucinatory, anesthetic and stimulating phenomena, also at the molecular level, many studies using LSD , Cocaine, Heroin (no ref in testo!)
- A deeper study of consciousness-altering drugs and their binding to Tubulin and Microtubules may help us to better understand the complex biological interface between conscious and unconscious states and the various forms of psychopathology in a deeper physical framework. We are interested in evaluating the existence of any correlation between alterations of conscious states and molecular interactions within the cell. A number of drugs are able to bind to Tubulin and modify its activation state [2][3]. In particular, we are interested in studying as Heroin, Cocaine and LSD, chosen as most representative among depressive, exciting and hallucinogen drugs, respectively, affect Central Nervous System (CNS) and the conscious state understand the implications of hallucinatory, anesthetic and stimulating phenomena, also at the molecular level, many studies using LSD , Cocaine, Heroin (no ref in testo!)
- To explore the potential binding of different psychoactive drugs we first performed a Molecular Dynamics (MD) procedure on the molecular structures of the chosen drugs with conformation optimization in water medium. Then we carried out docking procedures between MTs …. (manca tub in testo!) ..and drug structures. Both MD and docking procedures will be widely explored in the following. Aim of these computational procedures is to identify possible biophysical effects due to conformational changes that occur as a result of the interaction between the protein and the substance, and to identify binding sites of Tubulin and subsequently how these new possible interactions may be involved in the CNS. The study can therefore support the hypothesis on the origin of different biophysical behaviours in relation to conformational changes, and derive a set of reasonable assumptions about the function of MTs as structures capable of managing and communicating information in the conscious process.
- Besides of MD, structural bioinformatics deals with molecular docking, a method that predicts the strength of association or binding affinity between two molecules, often the binding features of small ligands to a protein target. This makes docking important in the modern drug design. Most biological functions are mediated by interactions between proteins and ligands. A protein can interact with other proteins, with nucleic acids, with small ligands (eg. metabolites or ions), with more ligands simultaneously. The binding with a ligand can induce a conformational change that influences the activity or accessibility of other binding domains. The protein-ligand interaction is dictated mainly by the complementary nature of the two compounds: charged ligands tend to be attracted by regions of opposite charges, and the shape of the ligand is reflected by the shape of the binding site (steric complementarity). This methodology is an important application when structural information of the intermolecular complex is not available and already deposited in the Protein Data Bank (PDB)
- we used the Ascalaph Designer software version 1.8.44, together with the packages Abalone (BioMolecula rmodeling) and PC GAMESS / Firefly (ab initio computational chemistry). This software combines Molecular Dynamics simulation in liquid phase (with explicit water molecules) with an interface for the quantum mechanics packages. Firefly QC package [8] is partially based on the GAMESS (US) [9] source code.
- In order to assess the significance of these findings we performed a dynamic simulation of the molecular structures of tubulin and MT subjected to different levels of e-m fields. We also compared them with CNT and BB structures. We adopted the Ascalaph simulation environment. It allows simulations of large molecular structures and many parameterizations. Ma di fatto come abbiamo usato ascalaph?? Forse sarebbe il caso di inserirlo!
- The construction of the ligands chemical structures was performed using the Ascalaph Designer ab-initio Free Drawing. The next step was the optimization, i.e. the energy minimization, of all the built chemical structures (energy minimization algorithm: conjugate gradient method, stop conditions: gradient value = 0.001 and iteration number = 100). For heroin 10 cycles of energy minimization were needed, and the value obtained for the energy minimization of the heroin molecule was E = 5.2133 Kcal/mol. For the cocaine molecule 5 cycles of energy minimization were needed, with final energy value E = 39.408694 Kcal/mol. For the LSD molecule 5 cycles of energy minimization were needed, obtaining E = 74.4203 Kcal/mol.
- molecular docking, a method that predicts the strength of association or binding affinity between two molecules, in general the binding orientation of small molecule drug to a protein target After building energy optimized molecules, we began the binding modelling using the HEX Protein Docking system [12] [13], a molecular docking software that allows both calculation and 3D visualization. HEX is able to predict the binding between a protein and a ligand, considering the latter as a rigid body; the interaction between molecules takes place solely on the basis of their 3D shape and of their electrostatic complementarity.
- Many algorithms of automatic molecular docking are able to generate a large number of possible structures, and to provide a criterion based on the energy of the intermolecular interaction, with which it is possible to determine the most stable complex. The purpose of an automatic molecular docking algorithm is therefore to generate and evaluate possible structures of intermolecular complexes. The most important goal is to develop methods capable to predict the geometry of binding through a function that estimates the affinity between target and ligand: this feature is generally referred to as the score function. Different types of score functions have been implemented: force field based, knowledge based, consensus scoring etc. [8] [9]. The first computationally efficient algorithm to determine the geometric complementarity between two molecular structures, able to solve the problem of rigid docking, was presented by Katchalski-Katzir et al. in 1992 This method consists of an automatic procedure that projects the molecule in a 3D grid, performing a distinction between surface and interior atoms. Then it calculates, using the Fourier transform, a correlation function that evaluates the overlapping degree of the molecular penetration relative to all the possible orientations of the molecule ligand.
- Illustration of spherical polar docking with respect to the intermolecular axis. An initial docking orientation may be defined by specifying which residues should be located at the local coordinate origin for each molecule, and by defining "interface residues" which will be located on the z-axis. The docking search may be restricted by defining a “range angle” for the receptor and/or ligand orientations. If range angles are defined, then the interface residues will always be constrained to appear within a spherical cone defined by the corresponding range angle. This illustration shows two range angles, each of 45 degrees. The calculation is arranged so that the intermolecular twist angle search is in the innermost loop of the search. The search around the twist angle may be accelerated using a 1D FFT. Alternatively, all three Euler angles assigned to the ligand can be searched together using a 3D FFT. In the Linux version, all five rotation angles may be searched together using a 5D FFT. However, this requires at least 1 gigabyte of memory to hold the very large 5D rotational grid Due to the special orthogonality property of the basis functions, the correlation (or overlap as a function of translation/rotation operations) between a pair of 3D functions can be calculated using expressions which involve only the original expansion coefficients. In many respects, this approach is similar to conventional fast Fourier transform (FFT) docking methods which use Cartesian grid representations of protein shape and other properties, and which then use translational FFTs to perform the docking correlations. However, the Cartesian grid approach only accelerates a docking search in three translational degrees of freedom whereas the SPF approach allows the effect of rotations and translations to be calculated directly from the original expansion coefficients. Even though the FFT part of a docking search may be fast, the overall speed of calculation still depends very much on the initial "set-up" costs and the final "post-processing costs" of filtering and perhaps clustering the results. Hex is fast because it uses FFT correlations as much as possible, and because the "set-up" costs are much lower in the SPF approach than in Cartesian grid-based approaches. It also turns out that the FFT part of the calculation maps very well to the GPU hardware. Thus, further speed-ups can be expected if you have a suitable graphics card. In the spherical polar approach, it is natural to assign the six rigid body degrees of freedom as five Euler rotation angles and an intermolecular separation. Thus, in complete contrast to Cartesian based FFT approaches, the rotational part of a docking search is the “easy bit” and modelling translations becomes the “hard part.” Fortunately, however, only a few translations (typically about 40 steps of 0.75 Ångstrom) are required to complete a six dimensional docking search. One advantage of the spherical polar approach is that it is easy to constrain the docking search to one or both binding sites, when this knowledge is available, simply by constraining one or two of the angular degrees of freedom. This can reduce docking times to a matter of minutes on a modern workstation. Hex generates several orientations with low RMS deviations from the correct (starting) orientation. However, you might object that the calculation was biased to find the right answer by restricting the search to the known binding sites.
- Clustering Docking Results Because Hex uses essentially a brute-force search approach to the docking problem, it is advisable to over-sample the search space rather than to risk missing a good solution by under-sampling the space. However, this can cause multiple similar but incorrect orientations (false-positives) to push good solutions down the list. By default, Hex uses a simple clustering algorithm to group spatially similar docking orientations. Each docking solution is first ordered by energy, and the lowest energy solution is made the seed orientation for the first cluster. The list is then searched down to a given depth for other similar orientations whose main-chain alpha-Carbon RMS deviation is within a given threshold (default 3Å RMS) of the seed orientation, and these orientations are then assigned to the first cluster. The process is then repeated starting from the next lowest unassigned orientation, until all solutions have been assigned to a cluster. The Cluster Window parameter may be used to control the search depth when looking for cluster members. Because clustering uses a simple but inefficient algorithm (rather like a “bubble-sort”), it is advisable use this parameter to limit the search depth if the number of saved solutions is large. Most of the algorithms of molecular docking generate a large number of possible structures, which must then be evaluated in order to select for subsequent analysis a smaller, but representative set of conformations that could be the most likely similar to the real "docking mode ". This is often realized using cluster analysis. Belonging to a cluster depends on how the element under consideration is far from the cluster. When comparing different conformations, the most commonly used measure is the RMSD (root mean square distance) between pairs of atoms: where Natoms is the number of atoms on which the RMSD is measured and di is the distance between the atom coordinates of the two structures
- The docking analysis was performed on two models, MTs and Tubulin. For the MT structure we adopted a portion of the 12-protofilaments left-handed Microtubule model developed by NANO-D research group at INRIA Grenoble-Rhone-Alpes [13], [14] and, for comparative purposes, of the Tubulin structure: we chose the refined structure of alpha-beta Tubulin stabilized with taxol, Bos Taurus organism (PDB code: 1JFF) [15]. We always refer to the αβ Tubulin heterodimer, usually considered as one unit.
- As a control ligand we used taxol, the principle used to inhibit cell mitosis, devoid of psychotropic characteristics, and typically associated with Tubulin in the databanks because of its stabilizing action [16]. Comparing MT and Tubulin, we note that taxol is present only at the level of a single CHAIN for each model, A in MT and B in Tubulin. Taxol shows different positions in Tubulin and MT, in fact takes contact with secondary structures only in MT. Taxol is a structure larger than the three considered drugs and shows a different docking location. Since eukaryotic cells greatly depend upon the integrity of microtubules and other cytoskeletal filaments to maintain their structure and essentially to survive, many plants produce natural toxins aimed at disrupting the microtubule network as a means of self-defense. Taxol, for example, is a toxic substance produced by a species of yew trees that increases microtubule polymerization (building a macromolecule) by binding to the filament and stabilizing it. Other natural toxins, such as the colchicine produced by the meadow saffron, destabilize microtubules and hinder their polymerization. Both kinds of events can be fatal to the affected cell, though in some circumstances, this can be beneficial to animals, as demonstrated by taxol, which is commonly used as a cancer medication.
- We observed that in MT the two ligands (hero e coca) are close to a kind of niche (perhaps the access way). Cocaine, compared to Heroin, seems to penetrate further into the structure and the binding site appears different. Analyzing the secondary structure of MT it is possible to note that Heroin assumes a more superficial position, moving in the direction of an alpha helix. By analyzing the structure through the Chain function it is shown that the two ligands are positioned both at Chain A. The third ligand, LSD, shows a completely different position than the other two ligands, assuming a superficial position in contact with two CHAIN and an alpha helix
- We observed that in MT the two ligands (hero e coca) are close to a kind of niche (perhaps the access way). Cocaine, compared to Heroin, seems to penetrate further into the structure and the binding site appears different. Analyzing the secondary structure of MT it is possible to note that Heroin assumes a more superficial position, moving in the direction of an alpha helix. By analyzing the structure through the Chain function it is shown that the two ligands are positioned both at Chain A. The third ligand, LSD, shows a completely different position than the other two ligands, assuming a superficial position in contact with two CHAIN and an alpha helix
- We observed that in MT the two ligands (hero e coca) are close to a kind of niche (perhaps the access way). Cocaine, compared to Heroin, seems to penetrate further into the structure and the binding site appears different. Analyzing the secondary structure of MT it is possible to note that Heroin assumes a more superficial position, moving in the direction of an alpha helix. By analyzing the structure through the Chain function it is shown that the two ligands are positioned both at Chain A. The third ligand, LSD, shows a completely different position than the other two ligands, assuming a superficial position in contact with two CHAIN and an alpha helix
- Different observations have been made for Tubulin: Cocaine and Heroin show similar behavior, in fact in Tubulin does not appear to come in contact with any secondary structure, is present in a niche and positioned between chain A and B. Heroin and Cocaine behave in a similar way in Tubulin. LSD takes similar position to the other ligands, but it is even more superficial and is only present at the level of CHAIN
- Different observations have been made for Tubulin: Cocaine and Heroin show similar behavior, in fact in Tubulin does not appear to come in contact with any secondary structure, is present in a niche and positioned between chain A and B. Heroin and Cocaine behave in a similar way in Tubulin. LSD takes similar position to the other ligands, but it is even more superficial and is only present at the level of CHAIN
- we have shown that the three chosen ligands, which play different roles in altering the state of consciousness, after the docking procedure appear to be positioned differently on the MT. In particular LSD shows a completely different position with respect to the other two ligands