Abstract
Artificial receptors have been employed in molecular recognition for a variety of biological applications. They have been used as materials for sensors, affinity separation, solid-phase extraction, and for research into biomolecular interaction. There have been a number of publications relating to the application of molecular modeling in the characterization of their affinity and selectivity; there are very few publications that discuss the application of molecular modeling to the computational design of artificial receptors. This chapter discusses recent successes in the use of computational design for the development of artificial receptors, and touches upon possible future applications, further emphasizing an exciting group of synthetic receptors—molecularly imprinted polymers.
Graphical Abstract
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- “ab initio”:
-
Latin term meaning “from the beginning”
- ΔE :
-
Binding energy
- 2-VP:
-
2-Vinyl pyridine
- 4-VP:
-
4-Vinyl pyridine
- AA:
-
Acrylic acid
- Accelrys DS viewer:
-
Modeling and simulation tools for drug discovery
- Agile molecule:
-
A three-dimensional molecular viewer which shows molecular models and provides geometry editing capabilities
- AHLs:
-
3-Oxo-C6-acyl-homoserine lactone
- ALM:
-
Allylamine
- AMBER:
-
Assisted model building with energy refinement refers to a MM force field for the simulation of biomolecules and a package of molecular simulation programs
- AMPSA:
-
2-Acrylamido-2-methyl-1-propanesulfonic acid
- B3LYP:
-
Becke 3-parameter, Lee, Yang and Parr, a density functional method
- Bite-and-Switch:
-
“Bite-and-Switch” is defined in terms of polymer’s ability to bind the template (bite) and generate the signal (switch)
- BLAs:
-
β-Lactam antibiotics
- B-Me:
-
Biotin methyl ester
- CAChe MOPAC:
-
A general-purpose semiempirical molecular orbital package for the study of chemical structures and reactions
- Cerius:
-
A software to visualize structures, predict the properties and behavior of chemical systems refine structural models (Molecular Simulations Inc.)
- Chem 3D:
-
A software that provides visualization and display of molecular surfaces, orbitals, electrostatic potentials, charge densities, and spin densities (http://www.cambridgesoft.com/)
- DFT:
-
Density functional theory
- Dielectric constant:
-
A measure of the ability of a material to store a charge from an applied electromagnetic field and then transmit that energy
- DMAEM:
-
Dimethyl aminoethyl methacrylate
- DOCK:
-
Program that addresses the problem of “docking” molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together
- DVB:
-
Divinylbenzene
- EGDMA:
-
Ethylene glycol dimethacrylate
- ELISA:
-
Enzyme-linked immunosorbent assay
- GAMESS:
-
General Atomic and Molecular Electronic Structure System: a general ab initio quantum chemistry package that can compute wave functions ranging from RHF, ROHF, UHF, GVB, and MCSCF
- Gibbs free energy:
-
The chemical potential that is minimized when a system reaches equilibrium at constant pressure and temperature
- GRID:
-
A computational procedure for detecting energetically favorable binding sites on molecules of known structure. The energies are calculated as the electrostatic, hydrogen bond and Lennard Jones interactions of a specific probe group with the target structure (Peter Goodford, Molecular Discovery Ltd)
- Gaussian:
-
“Ab initio” electronic structure program that originated in the research group of People at Carnegie-Melon. Calculate structures, reaction transition states, and molecular properties (http://www.gaussian.com)
- Gaussview:
-
Graphical user interface (GUI) designed for use with Gaussian for easier computational analysis
- HEMA:
-
Hydroxyethyl methacrylate
- His:
-
Histidine
- HOOK:
-
Linker search for fragments placed by MCSS
- HO-PCBs:
-
Hydroxy polychlorinated biphenyls
- HPLC:
-
High performance liquid chromatography
- HVA:
-
Homovanillic acid
- HyperChem:
-
A molecular modeling package for windows
- IA:
-
Itaconic acid
- k′:
-
Retention factor
- Leapfrog™:
-
A component of the SYBYL™ software package (Tripos) and is a second-generation de novo drug discovery program that allows for the evaluation of potential ligand structures
- LEGEND:
-
Atom-based, stochastic search
- Ligbuilder:
-
General-purpose structure-based drug design program
- LUDI:
-
Fragment-based, combinatorial search
- MAA:
-
Methacrylic acid
- Materials Studio:
-
Software for modeling/simulation of crystal structure, polymer properties, structure–activity relationships (http://www.accelrys.com/products/mstudio)
- MBAA:
-
N,N′-Methylenebisacrylamide
- MD:
-
Molecular dynamics
- MIC:
-
Molecularly imprinted catalysis
- MIP:
-
Molecularly imprinted polymer
- MM:
-
Molecular mechanics
- MMA:
-
Methylmethacrylate
- MMFF94:
-
A tool for conformational searching of highly flexible molecules
- MOE:
-
Molecular Operating Environment is a software system designed for computational chemistry
- Monte Carlo:
-
An algorithm which computes based on repeated random sampling to arrive at results
- MOPAC AM1:
-
AM1 is used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with respect to molecular geometry. MOPAC calculates the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers
- NAM:
-
A scalable molecular dynamics code that can be run on the Beowulf parallel PC cluster for molecular dynamics simulations on selected molecular systems
- NIP:
-
Non-imprinted polymer
- NVT-MD:
-
Molecular dynamics performed under constant number of atom, volume, and temperature ensemble
- OPA:
-
o-Phthalic dialdehyde
- OscailX:
-
Molecular modeling software, National University of Ireland (http://www.ucg.ie/cryst/software.htm)
- OTA:
-
Ochratoxin A
- PCFF:
-
Polymer consistent force field
- PCM:
-
Polarizable continuum model
- PCModel:
-
Structure building, manipulation, and display program which uses molecular mechanics and semiempirical quantum mechanics to optimize geometry. Available on PC (DOS and Windows), Macintosh, SGI, Sun and IBM/RS computers (Kevin Gilbert, Serena Software)
- PenG:
-
Penicillin G
- pK a :
-
Ionization constant
- PRO-LIGAND:
-
Fragment-based search
- Qm:
-
Mean absolute atomic charge
- QM:
-
Quantum mechanics
- RECON:
-
An algorithm for the rapid reconstruction of molecular charge densities and charge density-based electronic properties of molecules, using atomic charge density fragments precomputed from ab initio wave functions. The method is based on Bader’s quantum theory of atoms in molecules
- RESP:
-
Atomic partial charge assignment protocol
- SDIM:
-
Sulfadimethoxine
- SHAKE:
-
A molecular dynamics algorithm
- Simulated annealing:
-
A method that simulates the physical process of annealing, where a material is heated and then cooled leading to optimization
- SM2 :
-
Sulfadimidine
- SMZ:
-
Sulfamethazine
- SPROUT:
-
Fragment-based, sequential growth, combinatorial search
- SYBYL™:
-
A molecular modeling and visualization package permitting construction, editing, and visualization tools for both large and small molecules (www.tripos.com)
- T:M:X ratio:
-
Template monomer cross-linker ratio
- TAE:
-
Transferable atom equivalent
- TFMAA:
-
2-(Trifluoromethyl) acrylic acid
- THO:
-
Theophylline
- TQT1:
-
ToxiQuant T1 System
- UAHF:
-
United atom Hartree–Fock
- van der Waals:
-
Weak intermolecular forces that act between stable molecules
- VI:
-
1-Vinylimidazole
- VMD:
-
Visual molecular dynamics
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Subrahmanyam, S., Karim, K., Piletsky, S.A. (2012). Computational Approaches in the Design of Synthetic Receptors. In: Piletsky, S., Whitcombe, M. (eds) Designing Receptors for the Next Generation of Biosensors. Springer Series on Chemical Sensors and Biosensors, vol 12. Springer, Berlin, Heidelberg. https://doi.org/10.1007/5346_2012_22
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