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Computational Approaches in the Design of Synthetic Receptors

  • Sreenath SubrahmanyamEmail author
  • Kal Karim
  • Sergey A. Piletsky
Chapter
Part of the Springer Series on Chemical Sensors and Biosensors book series (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.

Graphical Abstract

Keywords

Artificial receptors Molecular dynamics Molecular imprinting Molecular modeling Sensors 

Acronyms and Further Descriptions

“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

pKa

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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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Sreenath Subrahmanyam
    • 1
    Email author
  • Kal Karim
    • 1
  • Sergey A. Piletsky
    • 1
  1. 1.Cranfield Biotechnology CentreCranfield UniversityBedfordshireUK

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