FBDD

19F-NMR has proved to be a detection mode in fragment-based drug discovery (FBDD) for studies of protein structure and interactions. 19F shows high sensitivity for NMR detection, and the exquisite sensitivity of 19F chemical shifts and linewidths to ligand binding all make it a valuable approach in FBDD.F (Fluorine) -Fragments can be used for 19F-NMR detection after binding to target proteins, and can be used as an effective 19F-NMR tool for FBDD.

MCE designs a unique collection of 5,017 F-fragments, all of which obey a heuristic rule called the “Rule of Three (RO3)”, in which molecular weight ≤300 Da, the number of hydrogen bond donors (H-donors) ≤3, the number of hydrogen bond acceptors (H-acceptors) is ≤3 and cLogP is ≤3. This F-fragments library is an important source of lead-like drugs.

Fragment-based drug discovery (FBDD) is well suited for discovering both drug leads and chemical probes of protein function; it can cover broad swaths of chemical space and allows the use of creative chemistry. Fragment-based drug discovery is well-established in industry and has resulted in a variety of drugs entering clinical trials, with two, vemurafenib and venetoclax, already approved. FBDD also has key attractions for academia. Notably, it is able to tackle difficult or novel targets for which no chemical matter may be found in existing HTS collections.

MCE designs a unique collection of 22,864 fragment compounds, all of which obey a heuristic rule called the “Rule of Three (RO3) ”, in which molecular weight ≤300 Da, the number of hydrogen bond donors (H-donors) ≤3, the number of hydrogen bond acceptors (H-acceptors) is ≤3 and cLogP is ≤3. This library is an important source of lead-like drugs.

Fragment-based drug discovery (FBDD) is well suited for discovering both drug leads and chemical probes of protein function. 3-dimensionality (3D) diversity is pivotal because the molecular shape is one of the most important factors in molecular recognition by a biomolecule. There is a developing appreciation that 3D fragments could offer opportunities that are not provided by 2D fragments.

MCE 3D Diverse Fragment Library consists of 5,400 non-flat fragment-like molecules (average Fsp3 value 0.58). More than 4,700 fragment compounds contain at least one chiral center in the structure. The key concepts that underlie the library design were 3D shape, structural diversity, reactive functionality and fragment-like. This 3D Diverse Fragment Library brings higher fragment hit optimization and increases the likelihood to find innovative hits in FBDD.

The MCE 1K Drug Fragment Library consists of 1,168 drug fragments. These drug fragments are derived from 2,946 FDA-approved drug molecules, and fragments from one drug can appear in other drugs, so these fragments are somewhat correlated with good PK/PD properties. Fragment-based screening can reserve enough chemical space for subsequent structural optimization. This compound library is an essential tool for drug screening based on FBDD (Fragment-Based Drug Discovery).

Fragment-based drug development (FBDD) is a strategy for drug discovery that can be applied both academically and commercially to enhance the identification of some non-drug targets. Fragment-based drug development has identified low molecular weight molecules (<300 Da) capable of binding to related macromolecules. These fragments can cover a wide chemical space and are easy to optimize later. Currently, several fragment-based drugs have entered clinical trials, of which two drugs, Vemurafenib and Venetoclax, have been approved for marketing.

Based on Tanimoto coefficient, MCE uses similarity algorithm to carefully select 2,302 high-structurally diverse 'RO3' compliant fragment molecules from large-scale fragment molecules, which can be applied to fragment based drug development.

Lysine is the second most common target residue used in the design of TCIs and related covalent ligands. Its appeal lies in its abundance in human proteins, which is approximately three times higher than that of cysteine (5.8% vs. 1.9%). This significantly increases the number of proteins suitable for covalent targeting, especially given that many human proteins lack ligandable cysteine residues. Moreover, it has been suggested that functional lysines have a lower probability of being replaced by mutation, as they often play a crucial role in catalysis by acting as bases or nucleophiles. Additionally, lysines are essential for maintaining the structural integrity of proteins and for regulating post-translational modifications (PTMs). Consequently, targeting lysine has garnered significant interest in recent years.

Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 445 fragment molecules which can target lysine residue and can be used for fragment-based covalent drug discovery.

Recently, significant advancements in tyrosine-targeting electrophiles have primarily occurred in the field of protein-protein interactions (PPIs), where cysteine residues are often underrepresented and novel chemistries are needed to address these interfaces. In this context, tyrosines are frequently more accessible compared to more buried binding sites. Moreover, they are commonly found at "hot spots," which are functional epitopes of PPIs, with 12.3% of the residues consisting of tyrosines. This prevalence is likely due to the hydrophobic nature of tyrosine, its ability to participate in aromatic π-interactions, and its capacity for hydrogen bonding. Beyond PPIs, some progress has also been made in covalent tyrosine targeting in other areas where more commonly addressed side chains are lacking. Even though tyrosine has a slightly lower pKa value compared to the protonated lysine side chain (approximately 10 vs. 10.5 for the unprotected amino acid side chains), significantly less progress has been made in the development of tyrosine-targeted covalent ligands compared to lysine. This is likely due to the reduced flexibility of the tyrosine side chain and the greater steric hindrance of its hydroxy group, which makes it more challenging to adopt suitable reaction geometries.

Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 124 fragment molecules which can target tyrosine residue and can be used for fragment-based covalent drug discovery.

Covalent inhibitors are small molecules that can bind specifically to target proteins through covalent bonds and inhibit their biological functions. Although for a long time, covalent targeting has been playing a subordinate role in drug discovery, with an increasing number of reports on successful clinical applications of such drugs, the potential of these agents is now being acknowledged.

Covalent ligands rely on reactive groups (“warheads”), and new warheads are key to expanding the scope of covalent modalities. Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 8,900 fragment molecules with covalent modification potential, which can target various reactive amino acid residues and can be used for fragment-based covalent drug discovery.

In the research of covalent inhibitors targeting serine and threonine, scientists have found that the nucleophilicity of these hydroxyl groups is significantly enhanced due to the influence of their surrounding environment. This results in higher activity during catalytic reactions. Aspirin, which targets the non-catalytic domain serine (Ser529 in human COX1) of cyclooxygenase, exerts its anti-inflammatory effect through covalent binding. β-lactam antibiotics, which targets the catalytic domain serine of penicillin-binding proteins, interferes with bacterial cell wall synthesis.

Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 3,300 fragment molecules which can target serine and threonine residues and can be used for fragment-based covalent drug discovery.