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Computational Approaches in the Design of Synthetic Receptors

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Book cover Designing Receptors for the Next Generation of Biosensors

Part of the book series: Springer Series on Chemical Sensors and Biosensors ((SSSENSORS,volume 12))

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.

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Abbreviations

“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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  1. Cranfield Biotechnology Centre, Cranfield University, Bedfordshire, MK43 0AL, UK

    Sreenath Subrahmanyam, Kal Karim & Sergey A. Piletsky

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    Sergey A. Piletsky

  2. , Cranfield Health, Cranfield University, Cranfield Campus, Cranfield, MK43 0AL, Bedfordshire, United Kingdom

    Michael J. Whitcombe

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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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