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Abstract

The physiochemical properties of drugs play an important role in the absorption and bioavailability of the drug substance and thus, to its effectiveness to reach to its target. Hence, these properties must be predicted at the preclinical stage of the drug development to avoid the chances of its failure at the later stage. The development in the field of computational biology has significantly reduced drug failures. In-silico approach to drug discovery and development now makes it possible to apply various techniques at the early stage of drug discovery to virtually screen the molecules which don’t appear to have good absorption/solubility properties. A lot of solubility models have been devised so far based on the experimentation as well as molecular descriptors. This paper elaborates the descriptive background of solubility prediction as well as various models developed in the recent years.




  1. Introduction:

In modern drug discovery, the techniques like combinatorial chemistry and high-throughput screening (HTS) have resulted large amount of compounds being tested in a day. However, the number of new molecular entities (NME) approved annually has not changed significantly over the last two decades according to the Center for Drug and Evaluation and Research of U.S.Food and Drug Administration (FDA)[1]. Investigation of the reasons that cause reduction in the drug likeliness of candidates may help us to discover developable drug candidates prior to expensive clinical trials.

In 1991, about 40% of drug candidate attrition was caused by adverse pharmacokinetics (PK) and bioavailability[2]. The development in the field of computational biology significantly reduced drug failures. In last five years, more than 158 drugs were approved by FDA for various diseases. QSAR and ADME-Tox like properties have been evaluated before clinical testing. However, poor Solubility and bioavailability is still a major factor that leads to drug attrition. The drug aqueous solubility and membrane permeability are the major factors affecting drug`s bioavailability[3].




  1. Prediction of Solubility of substance:

The solubility of organic molecules in water has a significant impact on many ADME-related properties of drugs, such as absorption, distribution, transport and eventually bioavailability[4]. The solubility of a neutral compound or of a compound in its non-ionized form is defined as the intrinsic solubility and normally represented as log S, where S is the concentration of the compound in mol/l in a saturated aqueous solution in equilibrium with the most stable form of the crystalline material. In practice, about 85% of drugs have log S between -1 and -5, and virtually none has a value<-6. Emperically, the logS range of -1 to -5 for most drugs reflects a compromise between the polarity necessary for reasonable aqueous solubility and the hydrophobicity necessary for the acceptable membrane transport[5].
Solubility and intestinal absorption are two counterparts applied in the Biopharmaceutics Classification System.

2.1 Biopharmaceutics Classification System:

The Biopharmaceutics Classification System is a system to differentiate the drugs on the basis of their solubility and permeability. It is a guide for predicting the intestinal drug absorption provided by the U.S. Food and Drug Administration[6]..



The classification:

According to the Biopharmaceutics Classification System, drug substances are classified as follows:


BCS suggests methods for classification according to dosage form dissolution together with solubility-permeability characteristics of the drug product
2.2 Types of Solubility:

There are mainly four types of solubility as described in the relevant literature:




Sr. No.

Solubility type

Description

1.

Intrinsic solubility

Solubility of a non-electrolyte or an electrolyte almost 100% in its neutral form is the concentration (mol/L) of its saturated solution in equilibrium with the solid phase.

2.

Thermodynamic Solubility

Solubility of a compound in a solvent can be defined as the maximum amount of the most stable form of the compound that can remain in solution in a given volume of the solvent at a given temperature and pressure under equilibrium condition.

3.

Apparent Solubility

Solubility of an electrolyte is a function of its intrinsic solubility, pH value and its pKa and is measured at a certain pH level.

4.

Kinetic Solubility

This type of solubility is the concentration when an induced precipitate first appears in a solution.


3. Types of Solubility models:

The aqueous solubility models can be categorized into two types, those correlated with experimentally determined properties and those not[7]. There are a number of ways in which the models can be classified. Even they can be classified on the basis of the characteristics of descriptors. They can even be classified in terms of various methods implemented to derive the model. The most specific classification can be:



  1. Solubility models based on experimental measurements.

  2. Solubility models devised using molecular descriptors.


3.1 In-silico models based on experimental measurements:

For a given solid state and solvent, the solubility S is almost exclusively dependent on the intermolecular adhesive interactions between solute-solute, solute-solvent and solvent-solvent molecules. That is to say the crystal packing, cavitation and solvation energy determine the intrinsic solubility of a compound[7]. A number of models have been devised so far, based on the equations generated on the various experimental properties including melting point, octanol-water partition coefficient, molecular weight, free energy of solvation, vapor pressure of pure substances, boiling point etc.



3.2 In-silico Solubility Models devised using Molecular Descriptors:

  • Molecular Descriptors:

The molecular descriptor is the final result of a logical and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment[8].

By applying the mathematical and/or logical operations on such structures, we can devise the short term that serve as the self explanatory describer of the elements and structure of the molecules. Such derivations are known as “Molecular Descriptors”.

Molecular descriptors are formulated by applying various concepts and principles from different theories/areas like Information theory, Quantum Chemistry, Organic Chemistry, Molecular Graph Theory etc.


  • Molecular descriptors and QSAR Modeling:

A molecular structure can be related to a particular effect in a biological system. But this relationship isn’t clear. If we can establish this relationship, we can use that information to our benefit. A number of efforts have been carried out to establish this relationship, which has led to the development of the various predictive models. If we take a series of chemicals and attempt to form a quantitative relationship between the biological effects (i.e. the activity) and the chemistry(i.e. the structure) of each of the chemicals, then we are able to form a Quantitative Structure Activity Relationship(QSAR)[9].

4. Solubility models developed in the recent years:

Several years back, the solubility models were being developed using huge datasets. There was a tendency among developers to use larger data set to develop the model. Gradually, some new developments have started the trend of designing and customizing new datasets according to the need and requirements.



The following is the summary of the solubility models developed in the last decade.

4.1. Summary of recent models for Aqueous Solubility Prediction[2002-2011][10]:

Year

Authors

Modeling method

Type of Descriptors

2002

Engkvist and Wrede

CNN

Topological and Constitutional

2003

Cheng and Merz

GA/MLR

Topological

2003

Wegner and Zell

CNN

Topological, Electronic

2003

Manallack et al

CNN

BCUT

2003

Schaper et al

MLR

HYBOT

2003

Yan and Gasteiger

CNN

3D

2003

Yan et al

CNN

3D

2004

Hou et al

MLR

Atom types

2004

Votano et al

CNN

Topological and Constitutional

2004

Bergstrom et al

PLS

2D and 3D

2004

Raevsky et al

MLR

HYBOT, Nearest neighbor similarity

2006

Hansen

ANN

PH dependent Aqueous solubility model

2008

Ducowicz

MLR

Drug like molecules

2010

Kramer

RF

Classification model

2010

Kramer

BRNN

Classification model


5. Available solubility data sources:

Despite the vital importance of the solubility data of different compounds from chemical, biochemical, pharmaceutical and industrial data sets, there is still a lack of fundamental solubility and mass-transfer data available in the literature to facilitate the development of solubility models[11].



Sr.No.

DataSet

Details

1.

Huuskonen

This is the most popular dataset used in the recently developed solubility models. It contains the structures in SMILES format.

2.

Delaney

Another well known data set containing 1144 law molecular weight compounds. Contains the structures in SMILES format with solubility in M/L

3.

PHYSPROP

It contains chemical structures, names and physical properties for over 41,000 chemicals. Physical properties collected from a wide variety of sources include experimental, extrapolated and estimated values. It is bundled with EPA's EPI Suite.

4.

AQUASOL

The latest(sixth) edition of the AQUASOL database, developed by Yalkowski[12]s of Aqueous Solubility contains almost twenty thousand solubility records for almost six thousand compounds. These data are extracted from over eighteen hundred scientific references.

5.

SOLUB

This Is comparatively new aqueous solubility database, on the Chemical Information System.  It provides detailed and extensive solubility data on more than 2,600 chemical substances

6.

MERCK

This dataset is from MERCK KGaA, which offers a diverse set of compounds including solubility. They provide perfect base for the data to be used in the Training set

7.

PubChem

It contains the datasets for three different domains: Compound, Bioassay, and Substance. Over 1.4 million  structures  from  Collaborative Drug Discovery (CDD) are now available in PubChem, including almost 94,000 novel structures.

8.

ChEMBL

It is the host of the dataset repositories for different applications with the extended searching routines to seek through the diverse set of data for finding ligand, target finding, browsing by drugs and searching various Assays.


6. List of packages for solubility prediction:

Sr. No.

Software

Method/

Descriptor

Commercial/ Freeware

1.

ACD/PhysChem




Commercial

2.

Slipper

MLR

Commercial

3

ADMET Predictor

Topological indices

Commercial

4

CSlogWS

Topological descriptors, ANN

Commercial

5

Material Studio

-

Commercial

6

COSMOTherm/COSMO-RS

MLR

Commercial

7

Qikprop

MLR

Commercial

8

ALOGPS 2.1

ANN

Freeware

9

ACD/logP

-

Freeware

10

LogP Caluculator from Molinspiration

-

Freeware

11

Discovery Studio

-

Commercial

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