Fragment-based lead discovery (FBLD) also known as fragment-based drug discovery (FBDD) is a method used for finding lead compounds as part of the

drug discovery In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate medications are discovered. Historically, drugs were discovered by identifying the active ingredient from traditional remedies or by ...

process. Fragments are small organic molecules which are small in size and low in molecular weight. It is based on identifying small chemical fragments, which may bind only weakly to the biological target, and then growing them or combining them to produce a lead with a higher affinity. FBLD can be compared with high-throughput screening (HTS). In HTS, libraries with up to millions of compounds, with molecular weights of around 500 Da, are screened, and nanomolar binding affinities are sought. In contrast, in the early phase of FBLD, libraries with a few thousand compounds with molecular weights of around 200 Da may be screened, and millimolar affinities can be considered useful. FBLD is a technique being used in research for discovering novel potent

inhibitor Inhibitor or inhibition may refer to: In biology * Enzyme inhibitor, a substance that binds to an enzyme and decreases the enzyme's activity * Reuptake inhibitor, a substance that increases neurotransmission by blocking the reuptake of a neurotra ...

s. This methodology could help to design multitarget drugs for multiple diseases. The multitarget inhibitor approach is based on designing an inhibitor for the multiple targets. This type of drug design opens up new polypharmacological avenues for discovering innovative and effective therapies. Neurodegenerative diseases like Alzheimer’s (AD) and Parkinson’s, among others, also show rather complex etiopathologies. Multitarget inhibitors are more appropriate for addressing the complexity of AD and may provide new drugs for controlling the multifactorial nature of AD, stopping its progression.

Library design

In analogy to the

rule of five Lipinski's rule of five, also known as Pfizer's rule of five or simply the rule of five (RO5), is a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has chemical pro ...

, it has been proposed that ideal fragments should follow the 'rule of three' (

molecular weight A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...

< 300,

ClogP In the physical sciences, a partition coefficient (''P'') or distribution coefficient (''D'') is the ratio of concentrations of a chemical compound, compound in a mixture of two immiscible solvents at partition equilibrium, equilibrium. This rati ...

< 3, the number of

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...

donors and acceptors each should be < 3 and the number of rotatable bonds should be < 3). Since the fragments have relatively low affinity for their targets, they must have high water solubility so that they can be screened at higher concentrations.

Library screening and quantification

In fragment-based drug discovery, the low binding affinities of the fragments pose significant challenges for screening. Many biophysical techniques have been applied to address this issue. In particular, ligand-observe nuclear magnetic resonance (NMR) methods such as water-ligand observed via gradient spectroscopy (waterLOGSY), saturation transfer difference spectroscopy (STD-NMR), ¹⁹F NMR spectroscopy and inter-ligand Overhauser effect (ILOE) spectroscopy, protein-observe NMR methods such as ¹H-¹⁵N

heteronuclear single quantum coherence The heteronuclear single quantum coherence or heteronuclear single quantum correlation experiment, normally abbreviated as HSQC, is used frequently in NMR spectroscopy of organic molecules and is of particular significance in the field of protein NM ...

(HSQC) that utilises isotopically-labelled proteins, surface plasmon resonance (SPR),

isothermal titration calorimetry Isothermal titration calorimetry (ITC) is a physical technique used to determine the thermodynamic parameters of interactions in solution. It is most often used to study the binding of small molecules (such as medicinal compounds) to larger macrom ...

(ITC) and

Microscale Thermophoresis Microscale thermophoresis (MST) is a technology for the Biophysics, biophysical analysis of interactions between biomolecules. Microscale thermophoresis is based on the detection of a temperature-induced change in fluorescence of a target as a fun ...

(MST) are routinely-used for ligand screening and for the quantification of fragment binding affinity to the target protein. At modern X-ray crystallography synchrotron beamlines, several hundred data sets of protein-ligand complex crystal structures can be obtained within 24 hours. This technology makes

crystallographic fragment screening Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics ( condensed matter physics). The w ...

possible, i.e. the use of

X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...

directly for the fragment screening step. Once a fragment (or a combination of fragments) have been identified, protein

is used to obtain structural models of the protein- complexes. Such information can then be used to guide

organic synthesis Organic synthesis is a special branch of chemical synthesis and is concerned with the intentional construction of organic compounds. Organic molecules are often more complex than inorganic compounds, and their synthesis has developed into one o ...

for high-affinity protein ligands and enzyme inhibitors.

Advantages over traditional libraries

Advantages of screening low molecular weight fragment based libraries over traditional higher molecular weight chemical libraries are several. These include: * More hydrophilic hits in which hydrogen bonding is more likely to contribute to affinity ( enthalpically driven binding). It is generally much easier to increase affinity by adding hydrophobic groups (

entropically Entropy is a scientific concept, as well as a measurable physical property, that is most commonly associated with a state of disorder, randomness, or uncertainty. The term and the concept are used in diverse fields, from classical thermodynam ...

driven binding); starting with a hydrophilic ligand increases the chances that the final optimized ligand will not be too hydrophobic (log P < 5). * Higher

ligand efficiency Ligand efficiency is a measurement of the binding energy per atom of a ligand to its binding partner, such as a receptor or enzyme. Ligand efficiency is used in drug discovery research programs to assist in narrowing focus to lead compounds with ...

so that the final optimized ligand will more likely be relatively low in molecular weight (MW < 500). * Since two to three fragments in theory can be combined to form an optimized ligand, screening a fragment library of N compounds is equivalent to screening N² - N³ compounds in a traditional library. * Fragments are less likely to contain sterically blocking groups that interfere with an otherwise favorable ligand-protein interaction, increasing the combinatorial advantage of a fragment library even further.

Library design

Library screening and quantification

Advantages over traditional libraries

See also

References

Further reading