Drug design and optimization

Designed to maximize efficiency in hit discovery and optimization, this compound library is built on a foundation of diverse Bemis-Murcko scaffolds, with each scaffold is represented by two specifically derived molecules. This strategy ensures broad chemical space through scaffold diversity while enabling preliminary functional group exploration. This approach provides early structure-activity relationship (SAR) insights for every scaffold, making it a valuable tool for accelerating drug discovery.

In modern drug discovery and chemical biology research, the azide group (-N₃) is an important functional moiety that is widely used in click chemistry, biomolecular labeling, drug delivery systems, and prodrug design due to its unique reactivity and bioorthogonality.

The MCE Azide Structural Compound Library contains 96 compounds featuring -N₃ functional groups. It is designed for the construction of click chemistry reaction systems and the subsequent development of functional molecules. This library enables the rapid assembly of targeting ligands, linkers, and functional molecular modules, thereby accelerating PROTAC assembly, optimization of antibody-drug conjugate (ADC) linkers, and the development of biological labeling probes. In addition, the high reaction selectivity and excellent biocompatibility of the azide group allow it to maintain stable reactivity even in complex biological environments, improving controllability and efficiency in drug design. It serves as an indispensable molecular tool in modern medicinal chemistry and chemical biology research.

Fragment-based drug discovery (FBDD) offers a strategic advantage by categorizing fragment hits according to their functional groups. This approach facilitates both the further optimization of these hits and the rational design of larger compounds through fragment combination. The amine functional group plays a vital role in drug development, as evidenced by its presence in many marketed drugs like Galantamine, Tacrine, and Rivastigmine. It is instrumental in enhancing solubility, improving bioavailability, and ensuring shelf-life stability—all critical factors for drug efficacy.

MCE offers a collection of 19,733 amine fragments for drug discovery. All of these compounds adhere to the Rule of Three (RO3) criteria for drug-likeness, which MCE offers a collection of 19,733 amine fragments for drug discovery, all of which stipulates a molecular weight ≤ 300 Da, ≤ 3 hydrogen bond donors, ≤ 3 hydrogen bond acceptors, and a cLogP ≤ 3.

In drug discovery and development (R&D) area, target binding and druggability optimization are core processes. Among these attributes, high solubility is critical for a compound to achieve druggability, as it directly impacts the progress of drug R&D. Superior solubility ensures the rapid dissolution and uniform distribution of drug molecules in vivo, thereby enhancing bioavailability and effectively mitigating issues such as suboptimal efficacy, increased dosage requirements, or exacerbated toxic and side effects arising from insufficient solubility.

From the perspective of medicinal chemistry, high-solubility drug fragments serve as high-quality "molecular building blocks". Based on these fragments, lead compounds with potential druggability can be rapidly screened out, which significantly shortens the drug R&D cycle and reduces R&D costs. Meanwhile, the high-solubility drug fragment library can provide diverse options for drug development in different therapeutic areas, offer solutions for the solubility defects of existing clinical drugs, and facilitate the development of novel, highly effective targeted drugs with higher bioavailability and better safety profiles.

MCE has collected and compiled 2,527 experimentally validated small-molecule fragments with high solubility. These fragments can be directly used for drug molecular design, providing high-quality pre-validated solubility fragments that significantly improve the efficiency of lead compound screening and accelerate the progress of drug R&D.

CRBN, namely cereblon, is the substrate recognition subunit of the E3 ubiquitin ligase complex in the ubiquitin-proteasome system. A CRBN ligand library refers to a collection of numerous fragments that can specifically bind to the CRBN protein.

These ligands are mostly designed based on validated CRBN-binding warheads and modified through AI-driven molecular generation optimization systems. They not only include classic lenalidomide-derived structures but also cover novel non-lenalidomide scaffolds. After drug-likeness filtering, these ligands exhibit structural diversity and favorable druggable properties. They can be further optimized and modified to facilitate the development of novel molecular glue degraders, accelerate the discovery of molecular glues that induce interactions between CRBN and new substrate proteins, and enable the exploration of novel CRBN substrates for identifying previously unknown CRBN-binding proteins.

MCE compiles 122 fragments that can specifically bind to the CRBN protein, with molecular weights ranging from 200 to 500. Compounds developed based on the library ligands target multiple disease targets such as cancer and autoimmune diseases, further advancing the development of Molecular Glues and PROTACs therapeutic agents.

The incidence and significance of central nervous system diseases are increasing at an alarming rate all over the world. Although substantial research efforts have been applied to develop new CNS-active drugs, only a few CNS disorders are addressed satisfactorily, while the remaining ones pose significant clinical challenges. Blood-brain barrier (BBB) permeability is one of the most important limiting factors in the design and development of novel CNS-targeted pharmaceuticals for the treatment of neurological disorders.

Carefully selected from the HTS Compound Collection to meet the parameters optimized for high BBB-permeability, our CNS Focused Screening Library comprising over 30,300 structurally-diverse and potentially CNS-active screening compounds. This original Screening Compound Library is aimed at supporting CNS drug design projects and HTS efforts in search for novel neurotherapeutics.

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 Lead-like Covalent Screening Library offers a valuable resource of 1,049 lead-like compounds with commonly used covalent warheads. These warheads, such as acrylamide, activated terminal alkyne, acyloxymethyl ketone, and boronic acid, are capable of reacting with specific amino acid residues, including cysteine, lysine, serine, and histidine. The inclusion of these reactive warheads in the library allows researchers to explore the potential of covalent inhibition, a powerful approach in drug discovery.

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 1,596 small molecules including identified covalent inhibitors and other bioactive molecules having common covalent reactive groups as warheads, such as acrylamides, activated terminal acetylenes, Sulfonyl fluorides/esters, cloracetamides, alkyl halides, epoxides, aziridines, disulfides, etc.

Sulfonyl fluoride (-SO₂F) overcomes the poor target selectivity of traditional covalent warheads that rely heavily on cysteine. With high stability and tunable electrophilicity under physiological conditions, it targets multiple nucleophilic residues including Lys, Tyr, Ser and His, offering expanded druggable space, lower off-target risks and prolonged efficacy. It is widely used in covalent inhibitors, molecular glues, PROTACs and chemical probes.

MCE has built a highly diverse sulfonyl fluoride fragment library with 1,162 structurally diverse, drug-like fragments. Designed for balanced reactivity, stability and compatibility, these molecules feature tunable electrophilicity, simple scaffolds and high derivatization potential. Combined with SuFEx click chemistry, the library enables efficient modular modification and rapid structure optimization.

Ideal for targeting non-cysteine residues, this library improves covalent screening and probe development efficiency, serving as a precise tool for early-stage covalent drug discovery and chemical biology research.

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.

Unnatural amino acids (UAAs), also referred to as non-canonical amino acids (ncAAs) or non-proteinogenic amino acids, are a class of amino acids that are distinct from the 20 standard natural amino acids. They can be obtained through chemical synthesis, biosynthesis, and other approaches, with structural diversity far exceeding that of natural amino acids. UAAs are mainly including naturally occurring non-canonical amino acids, chemically synthesized amino acids, and biosynthetic amino acids, which provide a molecular basis for protein function design.

UAAs exhibit significant value in multiple fields. They can optimize the pharmacokinetic properties of peptide drugs and peptidomimetics, modify enzyme functions and endow them with new biological activities, thereby overcoming the limitations of traditional peptide drugs and expanding the chemical space . Meanwhile, UAAs can serve as molecular probes to analyze protein-protein interactions and investigate the regulatory mechanisms of protein functions.

MCE has compiled a UAAs Fragment Library comprising nearly a thousand unnatural amino acid fragments with extensive coverage of chemical space and enhanced structural diversity. This compound library can be widely applied in peptide synthesis, drug design, and protein engineering.

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 6,078 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.

Research has shown that drugs targeting aging pathways demonstrate promising potential in models of age-related diseases such as Alzheimer's disease, cardiovascular diseases, metabolic syndrome, osteoarthritis, and various malignancies. This suggests that intervening in the biological processes of aging may enable synergistic prevention and treatment of multiple chronic diseases. Against the backdrop of the gradual elucidation of core aging mechanisms-including cellular senescence, telomere attrition, epigenetic dysregulation, and chronic inflammation anti-aging research has shifted from traditional phenotypic interventions toward targeting key pathways that regulate biological age.

The MCE Anti-Aging Compound Library Mini is precisely built upon this cutting-edge concept. It focuses on aging-related targets validated through genetic or functional studies, comprising 381 compounds designed to provide systematic research tools for aging biology and intervention strategy development. The library covers core mechanisms such as mTOR, SIRT, energy metabolism, clearance of senescent cells, optimization of mitochondrial function, and telomere maintenance. For each target, 1-5 compounds with clear activity and strong representativeness have been carefully selected, spanning the entire translational spectrum from preclinical tool molecules to clinically investigational drugs.

Targeted Protein Degradation (TPD) is a novel and promising approach to drug development. It shows great potential for targeting proteins traditionally considered "undruggable" due to the lack of enzymatic function and absence of binding sites by tagging them for degradation or recruiting natural degradation mechanisms.

Molecular glues are a type of small-molecule degraders that primarily induce novel interactions between E3 ubiquitin ligases and target proteins, forming ternary complexes that lead to protein ubiquitination and subsequent proteasomal degradation. Compared with PROTACs, molecular glues generally have lower molecular weights, higher cell permeability, and better drug-like properties. Additionally, the design of molecular glues is relatively simple, without the requirements for complex linkers and ligand optimization. As a result, molecular glues have gradually emerged as a promising therapeutic approach for various diseases.

Multiple types of molecular glues have been reported previously. Analysis of co-crystal complex structures reveals that CRBN-related molecular glues are more versatile. Therefore, MCE researchers select active molecules related to these targets as probes for artificial intelligence (AI) screening.Subsequently, molecular docking technology was used to verify whether the screened molecules retained the key pharmacophore features. Ultimately, we obtained 317 molecular glue analogs, and these compounds serve as powerful tools for the research of molecular glues.