Conformational AnalysisSystematic Method and Model-building Approach Pinky Sheetal V 1801110004 M.tech Bioinformatics
Contents• Introduction to Conformational Analysis• Search Methods• Systematic methods for exploring conformational space• Model building approach• Available Technologies• References
Conformational Analysis• Conformation generally means structural arrangement• Conformational analysis is needed to identify the ideal conformation of a molecule• The biological activity of molecules is strongly dependent on their conformation• Done by exploring the energy surface of a molecule and determining the conformation with minimum energy• Needed: – Conformational space – Search method – An energy determination method
Conformational Space• clash-free space - atoms are not in self-collision Conformational search methods• Systematic search algorithms• Model-building methods• Random approaches – Generates conformers by random perturbation of Cartesian coordinates or the torsion angles of rotatable bonds• Distance geometry – Determines the lower and upper distances for all pairs of atoms in the molecule and the distance matrix is generated• Molecular dynamics
Systematic Method• Simplest• Deterministic• Grid searchAssumption: All bond lengths and angles remain fixed throughout the calculation Identify all rotatable bonds Rotate bonds through 360degrees by fixed increments Advantages • A deterministic approach, hence Generate a new conformation a systematic exploration of conformational space Energy minimization • Can be used for small molecules or systems with 10-15 bonds Minimum energy conformation All possible torsion angles combinations have been generated and minimized
ShortcomingsCombinatorial explosion:Θ is the dihedral angle chosen for the bond iExample –• 3 rotatable bonds – 30 degree increment – Conformers generated = 1728 – Time = 29 min• 5 rotatable bonds – 30 degree increment – Conformers = 248832 – Time = 69 hours• Time for 7 rotatable bonds = 415 days• Explores large regions with high energy• Not good for highly flexible molecules Therefore its time consuming and cannot be used for large system
Search treeEliminates the time consuming energy minimization stage for structures that have a very highenergy or some other problem 0 Root node 1 3 2 4 13 15 14Conformers with severe intra-molecular clashes, i.e. interatomic van der Waals contactenergy greater than 10 kcal/mol are removed.
Model-building method• Construct conformations of molecules by joining together three-dimensional structures of molecular fragments• Assumptions:1. Each fragment must be conformationally independent of the other fragments in the molecule2. Conformations stored for each fragment must cover the range of structures that are observed in fully constructed molecules• Substructure search algorithm – Substructure searching is finding a mapping for a query to a target molecule. – In other words, no bonds are broken and no new bonds are formed.
Available technologies• CatConf, or ConFirm, from Accelrys that is part of the Discovery Studio pharmacophore modeling protocols and tools provides two different search modes, fast (systematic search) and best (distance geometry) .• The program systems CORINA and ROTATE available from Molecular Networks.• OMEGA from OpenEye Scientific Software is a fast systematic, knowledge-based method.• MacroModel from Schrodinger is a very well-known and widely used force field-based molecular modeling package and offers a variety of methods for conformation generation.• CONFORT was developed by Prof. Pearlman, University of Texas, Austin and is distributed by Tripos. CONFORT performs an exhaustive conformational analysis of a molecule.• Some open source packages, such as Open Babel (http://openbabel.org) or RDKit (http://www.rdkit.org), provide means to generate sets of molecular conformations.
References• Christof H. Schwab, Conformations and 3D pharmacophore searching, DOI: 10.1016/j.ddtec.2010.10.003• http://www.biochem.vt.edu/modeling/conformation.html• Elber, R. and Karplus, M. (1987) Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin, Science 235: 318-321.• Leach, A.R. (1991) A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules, in, Reviews in Computational Chemistry, Vol.2, Lipkowitz, K.B. and Boyd, D.B., eds. VCH Publishers, New York, pp. 1-55.• http://www.chem.memphis.edu/parrill/chem8711/2004/Conformational%20Search.pdf• I-Jen Chen and Nicolas Foloppe, Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening, J. Chem. Inf. Model. 2008, 48, 1773–1791• Molecular Modelling Principles and Applications, Andrew R. Leach, 2nd Edition, Prentice Hall