Bioreceptor Platform: A Macromolecular Bed for Drug Design

Asian J. Research Chem. 3(4): Oct. - Dec. 2010

ISSN 0974-4169

www.ajrconline.org

REVIEW ARTICLE

Bioreceptor Platform: A Macromolecular Bed for Drug Design Sandip N. Badeliya and Dhrubo Jyoti Sen

Department of Pharmaceutical Chemistry, Shri Sarvajanik Pharmacy College, Hemchandracharya North Gujarat University, Arvind Baug, Mehsana-384001, Gujarat, India *Corresponding Author E-mail: [email protected]

ABSTRACT:

Receptor based drug design now plays a major role in the drug discovery. It may be applied to drug design depends highly on the availability of the receptor information. Systematic identification of protein-drug interaction networks is crucial to correlate complex modes of drug action to clinical indications and is applied to drug design when receptor structure is identified or characterized by high-resolution X-ray crystallography, NMR spectroscopy techniques or electron cryomicroscopy. The X-ray structures of a receptor and ligand-receptor complex provide greater and also some useful information about the binding cavity. Since binding sites of the receptor are very stereospecific so ligand or the drug molecule is modified in silico to achieve a better fit of the drug molecule to the binding site. This type of ligand modification is carried out by using sophisticated molecular modeling softwares. Especially by combinatorial chemistry drug synthesis is carried out in highly efficient manner and in larger quantities also. Trial and error approach of the ancient time is now totally changed. The aim is to achieve a better and novel drug that bind to its particular receptor.

KEYWORDS: Receptor, Drug design, de novo drug design, molecular modeling, computer assisted drug design, docking.

INTRODUCTION:

For example, molecules were isolated from plant exudates, and one by one fragment which are devoid of any activity were discarded from that typical structure of the exudates. It was based on chemical structure of the lead compound and structure activity relationships were carried out on that lead compound. Effective molecule was obtained by serendipity (luck by chance) and intuition. Finally random screening of larger no. of compounds was carried out. It was really an unusual chemistry.

History of drug design Drug design, also sometimes referred to as rational drug design, is the inventive process of finding new medications based on the knowledge of the biological target. The drug is most commonly an organic small molecule which activates or inhibits the function of a biomolecule such as a protein which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves design of small molecules that are complementary in shape and charge to the biomolecular target to which they interact and therefore will bind to it. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is often referred to as computer-aided drug design1-3.

Structure activity relationships were carried out generally by homolog approach in which one molecule is replaced by another molecule. Another approach was the molecular fragmentation in which one or more fragment was removed from the molecule to get more potent compounds. Another approach was the molecular addition in which one or more molecule was added to get perfect binding of the ligand Drug design in the ancient times Traditional drug design approach was introduced in 1900 with the binding pocket of the receptor. Another approach A.D. It was actually based on the natural source. Molecules was the Isosteric replacement in which one or more atom were obtained especially from plant, animal, micro was replaced by another atom that has some desirable molecular and electronic structure. The aim of that SAR organisms and marine sources. study was to find more potent compounds that can be useful as the drug candidate. Some of the disadvantages of that design were it was more time consuming and more costly Received on 25.01.2010 Modified on 12.02.2010 too. Accepted on 20.03.2010 © AJRC All right reserved Asian J. Research Chem. 3(4): Oct. - Dec. 2010; Page 703-706

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some ligands merely block receptors without inducing any response (e.g. antagonists). Ligand-induced changes in receptors result in physiological changes which constitute the biological activity of the ligands. The shapes and actions of receptors are studied by X-ray crystallography, computer modeling and structure-function studies, which have advanced the understanding of drug action at the binding sites of receptors. Structure of the receptor:

Figure 1: Traditional approach in drug design Rational approach Rational approach is the mechanism based drug design or target based drug design in which the target site or the diseased state is considered and here no importance of the chemical structure. Hydrogen bonding, electronegativity values, potential energy, Anchoring sites, size etc. factors are considered. In the sense screening and synthesis are carried out by preplanning. Figure 3: Transmembrane receptor

Where, E=extracellular P=plasma membrane

space;

I=intracellular

space;

Depending on their functions and ligands, several types of receptors may be identified: Some receptor proteins are peripheral membrane proteins whereas many hormone and neurotransmitter receptors are transmembrane proteins. Some metabotropic receptors are coupled to G-proteins and affect the cell indirectly through enzymes which control ion channels. Whereas Ionotropic receptors contain a central pore which opens in response to the binding of ligand. Another major class of receptors is intracellular proteins such as those for steroid and intracrine peptide hormone receptors.

Figure 2: Rational approach in drug design

Biological target4,5 A biological target is a biopolymer such as a protein or nucleic acid whose activity can be modified by an external Various receptor beds: stimulus. The definition is context-dependent and can refer 1. Angiotensin converting enzyme receptor bed to the biological target of a pharmacologically active drug compound, or the receptor target of a hormone (like insulin). The implication is that a molecule is "hit" by a signal and its behavior is thereby changed. Biological targets are most commonly proteins such as enzymes, ion channels, and receptors. Receptor A receptor is a protein molecule, embedded in either the plasma membrane or cytoplasm of a cell, to which a mobile signaling (or "signal") molecule may attach. A molecule which binds to a receptor is called a "ligand" and may be a peptide (such as a neurotransmitter), a hormone, a pharmaceutical drug, or a toxin, and when such binding occurs, the receptor undergoes a conformational change which ordinarily initiates a cellular response. However,

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2. Acetylcholine esterase receptor bed

6. Insulin receptor bed

3. Adrenaline receptor bed

7. Glutamate receptor bed

4. Chloride ion channel receptor bed

8. Dopamine receptor bed

5. Gamma-Amino butyric acid

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9. Serotonin receptor bed

give enough encouragement about the rapid development of the structure-based drug design. Currently, methods that have been developed for structurebased drug design can be roughly divided into two categories. The first category is about finding of ligand molecules for a given receptor that is usually referred as database searching. In this case, a large number of potential ligand molecules are screened to find those fitting the binding pocket of the receptor. This method is usually known as ligand-based drug design. The key advantage of database searching is that it saves time. It also saves synthetic effort to obtain new lead compounds. Another category of structure-based drug design methods is about building of ligand molecules that is usually known as receptor-based drug design. In this case, ligand molecules are built up within the constraints of the binding pocket by putting small pieces in a stepwise manner. These pieces can be either atoms or fragments. The key advantage of such a method is that novel structures, not contained in any database, can be suggested. These techniques are raising much excitement to the drug design community.

Figure 4: Various receptor beds Drug design: Drug design, as described earlier, is the inventive process of finding new medications based on the knowledge of the biological target. There are two major types of drug design. The first is referred to as ligand-based drug design and the second, structure-based drug design. Ligand based drug design:6 This type of design relies on knowledge of other molecules that bind to the biological target. Other molecules may be used to derive a pharmacophore. A model of the biological target may be built based on the knowledge of what binds to it and this model may be used to design new molecular entities that interact with the target.

Structure based drug design:7-10 This type of design relies on knowledge of the 3D structure of the biological target. Using the structure of the biological Figure 5: Flow chart of two strategies of structure based drug target, candidate drugs with high affinity and selectivity to design the target may be designed. Identification of the receptor structure: The receptor One can find structure of the receptor by methods such as structure has been characterized by either high-resolution X-ray crystallography, Electron cryomicroscopy, or by X-ray crystallography or NMR spectroscopy techniques. NMR spectroscopy. If a structure of the target protein is The 3D structure information may be obtained either by X11-14 available then drug design process is carried out. The ray crystallography or by electron Cryomicroscopy . molecule which shows perfect bind to the receptor is taken and synthesized as a drug. If the structure of the receptor is X-ray crystallography not known, then based on the experimental structure of the It is a direct approach to obtain receptor structure at atomic related protein, it is not difficult to create a homology level. This method determines the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal model of the target receptor. and diffracts into many specific directions. From the angles Now a days information about 3D structures of bimolecular and intensities of these diffracted beams, a crystallographer target receptors has increased dramatically due to can produce a three-dimensional picture of the density of development of an experimental methods like X-ray electrons within the crystal. From this electron density, the crystallography and NMR spectroscopy. Also there is an mean positions of the atoms in the crystal can be increment in the information about the structural dynamics determined, as well as their chemical bonds, their disorder and electronic properties about ligand molecules. These all and various other information.

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Figure 6: X-ray analysis of receptor protein crystal This technique requires source rich in protein of interest. 3). Shoot many micrographs at different angles and focal planes. Various Steps are involved in this process. These include: First obtain protein crystals then collect diffraction spots after that known amino acids are positioned in electron density map then optimize match with diffraction pattern. Finally experimental electron density map gives accurate molecular structure of that receptor. Another technique that is used to determine 3D structure of the receptor is Electron Cryomicroscopy, pioneered by Henderson and Unwin. This technique involves following 4). Extensive digital process to obtain single averaged image. steps: Figure 7: Procedure for electron cryomicroscopy

1. Purify protein from source rich in it.

Benefits and disadvantages: It requires high expertise level. It requires source rich in protein of interest. Atomic resolution may not be achieved so far though possible theoretically. It gives insight into protein structure in the absence of X-ray crystallography. Challenges in drug design: Today pharmaceutical industry faces the biggest challenges. Amongst them one of the biggest challenges is the design and discovery of new drugs. Money and time must also be considered in the discovery process. Most drugs are designed by either structure modification of some known drugs, by using disease models screening of combinatorial libraries, or by therapeutic agents or vaccines that can be prepared by development of proteins. Newer methods also developed to identify or design de novo compounds that modify the activity of a target protein. These involve computerized methods.

2. Quickly freeze with protein embedded in membrane.

De novo drug design: De novo drug design is an iterative process in which the three- dimensional structure of the receptor is used to design newer molecules. The method involves determination of the structure of lead target complexes and the designing of modifications of the lead using molecular modeling. This process can also be used for the designing compounds of some new chemical classes

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that present similar substituents to the target using a template or scaffold, which is chemically distinct from previously characterized leads. This involves building some new molecules from scratch to fit the binding site of a protein. Often, this involves identifying molecular fragments that are complementary to particular parts of the binding site, and attempting to connect them into a single molecule. It is illustrated in the following figure:15 1. Given a protein structure

2. Build a model of binding site

Figure 10: Small molecule docked to a protein

Docking procedures 1. Manual docking: - It is carried out if the binding groups are known. Here ligand is coupled with its complimentary group that present in the binding site. 2. Automatic docking: - It is carried out if the binding groups are unknown. It is done by programme like Chem X. Here structure of target protein is loaded in to the computer and Docking analysis carried out automatically.

3. Construct a molecule that fits to the binding site

The whole protein looks like this, the ligand is shown in red colour20. If one draws the protein with its van der Waals surface, it notices that there is a small opening which is probably the place where the ligand entered the binding pocket. Figure 8: Procedure of de novo drug design

Docking: This approach starts with a database of some known molecules and attempts are done to place each one of the in the binding pocket of the receptor protein and, if any molecule is succeed, estimation of the affinity of the binding of that molecule with the receptor protein is done using a scoring function. In the end, a list of the bestbinding molecules for the protein being targeted is returned. Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. It is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs16-19.

Protein receptor

Ligand

Complex

Figure-11: Drug binding pocket of receptor

Figure 9: Schematic diagram illustrating the docking of a small molecule ligand to a protein receptor to produce a complex

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Apparently the receptor closed again and the molecule is information may in turn be used to design more potent and trapped in there. If one eat away some of the outer amino selective analogs. Protein ligand docking can also be used to predict acids, he can take a better look at the binding pocket or at a semi transparent binding pocket. Remove some more amino pollutants that can be degraded by enzymes. acids that are in the way and it'll look like this. QSAR and drug design: A quantitative structure-activity relationship (QSAR) shows an attempt that has been used to correlate structural properties or property descriptors of compounds with their activities. The physicochemical descriptors that include parameters like hydrophobicity, topology, electronic properties, and steric effects, are determined either empirically or more recently by computational methods. Activities used in QSAR include chemical measurements and biological assays. QSAR now a days are being applied in many disciplines, with many pertaining to drug design and environmental risk assessment. Scientists that involved in the researcher work have attempted to develop drugs based on QSAR for many years ago. When these efforts began to start, easy access to computational resources was not available, so attempts consisted primarily of statistical correlations of structural data with their biological activities. However, as access to high-speed computers and graphics workstations became commonplace, this field has evolved into rational drug design or computer-assisted drug design22. Computer-Assisted Design: Computer-assisted drug design (CADD), also referred as computer-assisted molecular design (CAMD), represents more recent applications of computers as tools in the drug design process. In considering this topic, it is important to emphasize that computers cannot substitute for a clear understanding of the system being studied. That is, a computer is only an additional tool to gain better insight into the chemistry and biology of the problem at hand.

Figure 12: Binding of ligand with the receptor

Scoring functions: When the receptor site is well defined, the program attempts to place atoms or fragments in the receptor site, and evaluates the fit between them. Each of the hits has to be judged to decide which one is the best from the possible outcomes is known as scoring. Scoring functions are fast approximate mathematical methods used to predict the strength of the non-covalent interaction (also referred to as binding affinity) between two molecules after they have been docked. Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug's biological target such as a protein receptor. It provides a way to rank placements of ligands relative to one another. Ideally, the score should correspond directly to the binding affinity of the ligand for the protein, so that the best scoring ligands are the best binders[21]. Program such as LEGEND, LUDI, Leap-Frog, SPROUT, HOOK, and PRO-LIGAND are used for the scoring function.

In most current applications of CADD, attempts are made to find a ligand (the putative drug) that will interact more effectively with a receptor that represents the biological target or the target site. Binding of ligand to the receptor may include hydrophobic, electrostatic, and hydrogenbonding interactions. Also solvation energies of the ligand and receptor site are important because partial to complete desolvation must occur prior to binding.

This approach to CADD method optimizes the fit of a ligand in a receptor site. However, optimum fit in a target site does not guarantee that the desired activity of the drug will be enhanced or that undesired side effects will be Application of the docking:21 diminished. Also this approach does not consider the Docking combined with a scoring function can be pharmacokinetic properties of the drug. used quickly for screening large databases of potential drugs in silico to identify molecules that are likely to bind The approach used in CADD is dependent upon the amount to protein target in a highly efficient manner. of information that is available about the ligand and Also docking can be used to predict in where and receptor. Ideally, one would have 3-dimensional structural in which relative orientation a ligand binds to a protein information for the receptor and the ligand-receptor (also referred to as the binding mode or pose). This complex from X-ray diffraction or NMR. The ideal is

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seldom realized. In the opposite extreme, one may have no experimental data to assist in building models of the ligand and receptor, in which case computational methods must be applied without the constraints that the experimental data would provide.

Figure 13: Conceptual basis of CADD

Based on the information that is available, one can apply either ligand-based or receptor-based molecular design methods. The ligand-based approach is applicable when the structure of the receptor site is unknown, but when a series of compounds have been identified that exert the activity of interest. To be used most effectively, one should have structurally similar compounds with high activity, with no activity, and with a range of intermediate activities. In recognition site mapping, an attempt is made to identify a pharmacophore, which is a template derived from the structures of these compounds. It is represented as a collection of functional groups in three-dimensional space that is complementary to the geometry of the receptor site. In applying this approach, conformational analysis will be required, the extent of which will be dependent on the flexibility of the compounds under investigation. One strategy is to find the lowest energy conformers of the most rigid compounds and superimpose them. Conformational searching on the more flexible compounds is then done while applying distance constraints derived from the structures of the more rigid compounds. Ultimately, all of the structures are superimposed to generate the pharmacophore. This template may then be used to develop new compounds with functional groups in the desired positions. In applying this strategy, one must recognize that one is assuming that it is the minimum energy conformers that will bind most favorably in the receptor site. In fact, there is no a priori reason to exclude higher energy conformers as the source of activity23. The receptor-based approach to CADD applies when a reliable model of the receptor site is available, as from Xray diffraction, NMR, or homology modeling. With the availability of the receptor site, the problem is to design ligands that will interact favorably at the site, which is a docking problem24.

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CONCLUSION:

20. Bohm HJ. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comp Aided Mol Des 1998; 12(4):309–23. 21. Joseph-McCarthy D, Baber JC, Feyfant E, Thompson DC, Humblet C. Lead optimization via high-throughput molecular docking. Current opinion in drug discovery and development; 2007; 10(3):264–74. 22. Foloppe N, Hubbard R. Towards predictive ligand design with free-energy based computational methods. Curr Med Chem; 2006; 13(29):3583–608. 23. Muegge I. PMF scoring revisited. J Med Chem 2006; 49(20):5895–902. 24. Suresh PS, Kumar A, Kumar R, Singh VP. An in silico approach to bioremediation: laccase as a case study. J Mol Graph Model 2008; 26(5):845–9.

Drug target especially receptor plays an essential role in the rational drug design to design new drugs that perfectly bind to the receptor. Identification of each and every molecule and synthesize them as a drug is a time consuming task and costly also. By using CADD methods, molecular modeling software structure can be modified and identified which one is the best and then the best possible structure is synthesized as a drug. Docking predicts the binding orientation of small molecule to their protein targets and predicts the affinity and activity of the small molecule. Hence these all plays an important role in the rational design of drugs.

REFERENCES: 1.

2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

13. 14. 15. 16. 17. 18.

19.

Block JH, Beale JM. Wilson and Giswold’s textbook of organic medicinal and pharmaceutical chemistry; Computational Chemistry and Computer Assisted Drug Design: Structure based drug design and Pharmacophore perception. Chapter 28,11: pp. 939-945. Raffa RB, Porreca F. Thermodynamic analysis of the drugreceptor interaction. Life Sci. 1989; 44(4):245–58. Moy VT, Florin EL, Gaub HE. Intermolecular forces and energies between ligands and receptors. Science 1994; 266(5183):257–9. Wang R, Gao Y, Lai L, Ligbuilder: A Multi-Purpose Program for Structure-Based Drug Design. Journal of Molecular Modeling 2000;6:498–516 Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nat Rev Drug Discovery 2005; 4(8):649–63. Jorgensen WL. The many roles of computation in drug discovery. 2004; 303(5665): 1813–18. Hille B. Ion channels of excitable membranes: Structure of channel proteins Chapter 13. Sinauer Associates Inc. 1996; 3. Hollmann et al. Cloning by functional expression of a member of the glutamate receptor family 1989; 342:643-648. Hollmann et al. N- glycosylation site tagging suggests a three transmembrane domain topology for the glutamate receptor GluR1. Neuron; 1994; 13:1331-43. Unwin N. The Croonian Lecture 2000. Nicotinic acetylcholine receptor and the structural basis of fast synaptic transmission. Phil Trans R Soc London. B Biol Sci 2000; 355:1813-29. Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struct Biol; 1996; 6(3):402–6. Kitchen DB, Decornez H, Furr JR, Bajorath J Docking and scoring in virtual screening for drug discovery: methods and applications. Nature reviews. Drug discovery; 2004; 3(11):935– 49. Jorgensen WL. Rusting of the lock and key model for proteinligand binding. Science; 1991; 254(5034):954–5. Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol, 2004; 337(5):1161–82. Jain AN. Scoring functions for protein-ligand docking. Curr Protein Pept Sci; 2006; 7(5):407–20. Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins Structure Function and Bioinformatics; 2007; 69:704. Robertson TA, Varani G. An all-atom distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins; 2007; 66(2):359–74. Rajamani R, Good AC. Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development. Current opinion in drug discovery and development; 2007; 10(3):308–15. Seifert MH, Kraus J, Kramer B. Virtual high-throughput screening of molecular databases. Current opinion in drug discovery and development; 2007; 10(3): 298–307.

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