fragments

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 5,023 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.

The MCE 1K Drug Fragment Library consists of 1,000 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 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.

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 2,323 high-structurally diverse 'RO3' compliant fragment molecules from large-scale fragment molecules, which can be applied to fragment based drug development.

The most prominent mechanism of action of kinase inhibitors is their competition with ATP by binding to the hinge region of the kinase protein. Once the kinase is blocked by an inhibitor, it loses the ability to transfer phosphate groups from ATP to other molecules, resulting in the loss of kinase activity.

The hinge-binding region of kinase inhibitors mimics the interaction pattern between the ATP nucleobase and the kinase. MCE extracted thousands of kinase inhibitors from the ChEMBL database and isolated their molecular fragments. In certain cases, the amino and amide groups on the molecular fragments are crucial for binding in the hinge region. Therefore, we enhanced the diversity of the collected results by adding these two groups to unoccupied positions on the ring system. Subsequently, the fragments were assessed for their hinge region binding ability via docking at distinct kinases, we also applied pharmacophore constraints to ensure interactions with key amino acids in the kinase hinge region, ultimately obtaining kinase-related molecular fragments.

MCE provides over 10,000 kinase fragment molecules that meet the above requirements and are available off the shelf, serving as an effective tool for screening and developing drugs targeting kinases.

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.

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 22,824 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.

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.

Different functional groups confer unique chemical properties and reactivity characteristics to compounds. The presence of these functional groups not only affects the physical properties of the compounds, such as solubility and boiling point, but also determines their chemical reactivity and potential applications in chemical synthesis.

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 4,900 multifunctional covalent fragments.

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. Currently, cysteine is the most common covalent amino acid residue in a variety of covalent drugs, and various warheads have been developed that can react with cysteine, providing the key building blocks for covalent drugs to form covalent bonds.

To meet the development needs of covalent inhibitors targeting cysteine, MCE has designed a unique collection of 3,358 fragments with different covalent warheads that target cysteine. The MCE Cysteine Targeted Covalent Fragment Library is designed using the following covalent warheads: Acrylamides, Propiolic acid ester, Dimethylamine functionalized acrylamides, Chloroacetamides, Acrylonitrile, 2-Cyanoacrylamide, Aziridine, Haloacetamide, etc. All fragments are pre-filtered with the Rule of Three restrictions which can be used for fragment-based covalent drug development.

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.

Macrocycles are promising scaffolds for the design of novel RNA targeting molecules. This collection of macrocycles for RNA consists of very diverse, drug-like molecules which incorporate certain known RNA-recognition elements (e.g. nucleobase ring systems and analogs) distributed within macrocyclic rings or peripheral fragments. As macrocyclic molecules tend to be larger than traditional screening molecules, it is vital to carefully assess and control their physicochemical properties. All macrocycles have been tested for aqueous and DMSO solubility with cutoffs applied at 10 mM in DMSO and 50 µM in PBS (pH 7.4); PAMPA permeability has also been tested for representative set of macrocycles.

Protein protein interactions (PPI) have pivotal roles in life processes. The studies showed that aberrant PPI are associated with various diseases. However, the design of modulators targeting PPI still faces tremendous challenges, such the difficult PPI interfaces for the drug design, lack of ligands reference, lack of guidance rules for the PPI modulators development and high-resolution PPI proteins structures.

The PPI Library comprises molecules of various sizes, frameworks, and shapes ranging from fragment-like entities to macrocyclic derivatives designed as secondary structure mimetics or as epitope mimetics. The designs cover β-turn / loop mimetics and α-helix mimetics. Since helices present at the interface in 62% of all protein-protein interactions. This library focused on designs including mimics with the substitution geometry of an a-helices, as well as designs that mimic the location of “hot-spot” side chains in helix-mediated PPIs.

Small molecule covalent inhibitors, or irreversible inhibitors, are a type of inhibitors that exert their biological functions by irreversibly binding to target through covalent bonds. Compared with non-covalent inhibitors, covalent inhibitors have obvious advantages in bioactivity, such that covalent warheads can target rare residues of a particular target protein, thus leading to the development of highly selective inhibitors and achieving a more complete and continued target occupancy in living systems. In recent years, the distinct strengths of covalent inhibitors in overcoming drug resistance had been recognized. However, toxicity can be a real challenge related to this class of therapeutics due to their potential for off-target reactivity and has led to these drugs being disfavored as a drug class. The drug design and optimization of covalent inhibitors has become a hot spot in drug discovery.

MCE covalent inhibitor library contains 3,023 small molecules including identified covalent inhibitors and other molecules having common covalent reactive groups as warheads, such as acrylamides, activated terminal acetylenes, sulfonyl fluorides/esters, cloracetamides, alkyl halides, epoxides, aziridines, disulfides, etc.

MCE Covalent inhibitor Library plus, with more powerful screening capability, further complement Covalent inhibitor Library (HY-L036) by adding some fragment compounds with covalent warheads.

MCE Seamless DNA Assembly Plus Kit contains an optimized mix of recombinase, reaction buffer, and additional cofactors that significantly improve the cloning efficiency and tolerance to impurities. This product can complete multiple DNA fragments recombination and takes only 5 minutes for single fragment, and the positive rate is more than 95%.

RNase III is a specific exonuclease expressed in E.coli that can cleave dsRNA into 12-15 bp dsRNA fragments.

MCE Agarose can be made into 0.5-2.5% agarose gel according to different needs and can resolve DNA and RNA fragments from 50-15,000 bp.

MCE Seamless DNA Assembly Ultra Kit is a next-generation recombinant cloning kit that allows the recombination of single or multiple DNA fragments in a single reaction.

Bst DNA Polymerase large fragment is a part of Bacillus stearothermophilus DNA polymerase, which is derived from E. coli strain. It is expressed in E. coli and purified and isolated multiple times.