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Pathways Recommended:	Antibody-drug Conjugate/ADC Related

Results for "

Rational drug design

" in MedChemExpress (MCE) Product Catalog:

By Targets:	Aryl Hydrocarbon Receptor (1) Bacterial (1) Beta-lactamase (1) Cholinesterase (ChE) (1) Cytochrome P450 (1) HIV (1) Interleukin Related (1) Ser/Thr Protease (1) Thrombin (1)
By Research Areas:	Infection (2) Inflammation/Immunology (1) Metabolic Disease (1) Neurological Disease (1)

Inhibitors & Agonists

Screening Libraries

Peptides

Targets Recommended: Drug Intermediate Drug Isomer Drug Derivative Drug Metabolite Antibody-Drug Conjugates (ADCs) Peptide-Drug Conjugates (PDCs) Radionuclide-Drug Conjugates (RDCs) Drug-Linker Conjugates for ADC ADC Linker

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-147128

PY109	Aryl Hydrocarbon Receptor Cytochrome P450 Interleukin Related	Inflammation/Immunology
PY109 is an orally active and highly selective aryl hydrocarbon receptor (AHR) agonist. PY109's EC₅₀ values in human-derived HepG2 and mouse Hepa-1c1c7 cells are 1.2 nM and 1.4 nM respectively. PY109 significantly upregulates the expression of CYP1A1 and IL-22, and inhibits the expression of IL-17A. PY109 significantly improves colitis in mice. PY109 can be used for research on colitis .

HY-P11260

MD5	Ser/Thr Protease Thrombin	Metabolic Disease
MD5 is a selective TMPRSS6 mimetic peptide inhibitor with an IC₅₀ for recombinant human TMPRSS6 protein of 22 nM and a K_i of 3.4 nM. MD5 exhibits the significantly reduced inhibitory effect on Matriptase, with an IC₅₀ of 352 nM and a K_i of 99.2 nM. MD5 exhibits good target specificity and only has a weak inhibitory effect on thrombin (Thrombin), with K_i of 120 nM. MD5 demonstrates good initial drugability and can be used for the study of iron overload diseases (such as hereditary hemochromatosis, β-thalassemia) .

HY-168189

HIV-1 inhibitor-76	HIV	Infection
HIV-1 inhibitor-76 (compound 9t-2) is a non-nucleoside reverse transcriptase inhibitor of HIV-1. HIV-1 inhibitor-76 can be used in anti-HIV research .

HY-179709

NDM-1-IN-12	Beta-lactamase Bacterial	Infection
NDM-1-IN-12 (Compound 10c) is an inhibitor of NDM-1 metallo-β-lactamase, with an IC₅₀ value of 9 nM. NDM-1-IN-12 effectively reverses bacterial resistance to β-lactam antibiotics and shows an additive effect when used in combination with antibiotics and SBL inhibitors. NDM-1-IN-12 can be used in the research of anti-multi-drug resistant bacteria .

HY-179620

AChE-IN-99	Cholinesterase (ChE)	Neurological Disease
AChE-IN-99 (Compound 5a) is an AChE inhibitor. AChE-IN-99 can be used for the research of Alzheimer's disease .

Cat. No.	Product Name

HY-L236

Amine Fragment Library	19,532 compounds
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 19,532 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 19,532 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.

Amine Fragment Library

19,532 compounds

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 19,532 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 19,532 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.

HY-L941

Allosteric Modulator Lead‑like Compound Library	4315 compounds
Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery. MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Å², rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets. This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Allosteric Modulator Lead‑like Compound Library

4315 compounds

Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery.

MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Å², rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets.

This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Cat. No.	Product Name	Target	Research Area

HY-P11260

MD5	Ser/Thr Protease Thrombin	Metabolic Disease
MD5 is a selective TMPRSS6 mimetic peptide inhibitor with an IC₅₀ for recombinant human TMPRSS6 protein of 22 nM and a K_i of 3.4 nM. MD5 exhibits the significantly reduced inhibitory effect on Matriptase, with an IC₅₀ of 352 nM and a K_i of 99.2 nM. MD5 exhibits good target specificity and only has a weak inhibitory effect on thrombin (Thrombin), with K_i of 120 nM. MD5 demonstrates good initial drugability and can be used for the study of iron overload diseases (such as hereditary hemochromatosis, β-thalassemia) .

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BODIPY 493/503 purchased from MedChemExpress. Usage Cited in: Nat Commun. 2025 Feb 1;16(1):1241. [Abstract]

MedchemExpress Validation 01

Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature. Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature. Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature.

BODIPY 493/503 purchased from MedChemExpress. Usage Cited in: Nat Commun. 2025 Feb 1;16(1):1241. [Abstract]

MedchemExpress Validation 01

MedchemExpress Validation 03

Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred

MedchemExpress Validation 04

MedchemExpress Validation

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