Virtual Screening

“Finding the Most Suitable Drug from Tens of Millions or hundreds of millions of drugs without making invivo tests in labs is what Virtual Screening is all about, Some researchers would prefer DeNovo drug discovery, however the evidence based Discovery will happen through Virtual Screening”

Feras Naser

Important Tools

PyMol

PyMOL is the industry-standard open-source tool for high-quality 3D molecular visualization and rendering; for more advanced, immersive analysis, platforms like ChimeraX offer superior handling of large assemblies (like cryo-EM data) and VR support.

TBC

TBC

AutoDock Vina

his is one of the most widely cited open-source docking engines, prized for its speed and reliability in predicting how small molecules bind to proteins using a sophisticated “iterative local search” algorithm.

TBC

TBC

Shrodinger Glide

Known as the “gold standard” for commercial molecular docking, Glide provides unparalleled accuracy by using a grid-based method to exhaustively sample ligand conformations and calculate precise binding energetics.

TBC

TBC

ChEMBL Bioactives

2.9 million molecules with known biological activity.

TBC

TBC

SureChEMBL 2.0

Billions of structures extracted from worldwide patents, identifying novel competitive spaces.

TBC

TBC

TTD (Therapeutic Target Database)

40,000 drugs with multidimensional activity data

TBC

TBC

Drug Repurposing - Essential Step

TargetMol or Selleckchem FDA-Approved Library: These contain ~3,000–4,000 compounds that are already safety-cleared.

DrugBank Online: You can download the 3D structures of FDA-approved and “Investigational” drugs. This is ideal for identifying existing drugs that might have off-target c-Met inhibitory activity.

Chemical Libraries

High Priority Strategic Libraries

These are Strategic Libraries to Find Binding Affinity with  KARS Target. In this section, there will be other libraries that target various diseases. 

KRAS-Targeted Library

ChemDiv Specifically designed for G12C, G12D, and G12V pockets.

CNS MPO Lead-like Library

ChemScene

Optimized for Blood-Brain Barrier (BBB) permeability.

Covalent Fragment Library

Enamine

Ideal for irreversible inhibition of “shallow” oncology targets.

SIRT/Epigenetic Library

SelleckChem

Targets aging pathways and longevity (Sirtuins, HDACs).

DNA-Encoded Library (DEL)

WuXi AppTec/HitGen

Billions of compounds for screening “undruggable” PPIs.

Senolytic-Focused Library

Life Chemicals

Targets pathways involved in cellular senescence.

 

Macrocycles Library

Broad Institute/ChemDiv

For large, flat protein-protein interactions in oncology.

Blood-Brain Barrier (BBB) Set

Otava Chemicals

Curated for high CNS penetration (Neurodegeneration).

Kinase Inhibitor Library

MedChemExpress

Essential for oncology signaling pathways.

Molecular Glue Library

Monte Rosa/Enamine

Targeted protein degradation (TPD) for oncology.

ZINC22 (Virtual)

UCSF (Shoichet Lab)

>30 billion “make-on-demand” molecules for virtual screening.

FDA-Approved Drug Library

Prestwick

Drug repurposing (fast-tracking for neuro diseases).

Natural Product Library

Analyticon

Rich in complexity for longevity and metabolic health.

Protein-Protein Interaction (PPI)

Life Chemicals

Focused on disrupting oncogenic complexes.

Fragment-Based Library

Charles River

Finding “seeds” for difficult pockets in neuro targets.

Autophagy Modulator Library

SelleckChem

Targets protein clearance (Neurodegeneration).

Metabolism/mTOR Library

ApexBio

Central to longevity and cancer cell growth.

RNA-Binding Library

OTAVA

Targeting the “dark matter” of the genome in oncology.

Ubiquitin Library

Bio-Techne

For E3 ligase ligands and protein degraders.

Mitochondrial Targeted Set

ChemDiv

Focus on energy production and longevity.

GPCR Targeted Library

Eurofins

Key for signaling in the central nervous system.

Ion Channel Library

Cayman Chemical

Critical for neuro-excitability and pain

3D-Diversity Library

ChemBridge

For targets where “flat” molecules fail

Induced Proximity Library

Arvinas/Commercial

Focus on PROTACs and molecular glues.

Reactive Fragment Library

Scripps Research

For covalent mapping of new oncology pockets.

Oncology & Signalling

  1. Aurora Kinase Set (Targeting mitosis)
  2. BCL-2 Family Library (Apoptosis regulators)
  3. HSP90 Focused Library (Chaperone proteins in cancer)
  4. STAT3 Inhibitor Library (Transcription factor targeting)
  5. DNA Repair Library (PARP and DDR inhibitors)
  1. Methyltransferase Library (Epigenetic oncology)
  2. Bromodomain (BET) Library
  3. Wnt/Beta-Catenin Library
  4. Tyrosine Kinase Library (RTK focused)
  5. Angiogenesis Library (VEGF/VEGFR targets)
  1. p53-MDM2 PPI Library
  2. Chemokine Receptor Library
  3. Phosphatase Library (Targeting “undruggable” phosphatases)
  4. Glycomimetic Library (Cancer metastasis)
  5. Peptidomimetic Library (Mimicking alpha-helices in PPIs)
  1. Cysteine Protease Library (Cathepsin targets)
  2. Serine Protease Library
  3. Matrix Metalloproteinase (MMP) Library
  4. PI3K/Akt/mTOR Pathway Library
  5.   MAPK Pathway Library
  1. Ras-Raf-MEK-ERK Focused Library
  2. Checkpoint Inhibitor Small Molecule Library
  3. Hypoxia-Inducible Factor (HIF) Library
  4. Tumor Microenvironment (TME) Library
  5. Ferroptosis Inducer Library (New oncology modality)

Longevity & Metabolic Health

  1. AMPK Activator Library (Metabolic longevity)
  2. NAD+ Boosting Library (Sirtuin precursors)
  3. FoxO Transcription Factor Library
  4. Lipid Metabolism Library
  5. Autophagy Enhancer Library
  1. Senomorphic Library (Suppressing SASP)
  2. Glucocorticoid Receptor Library
  3. Retinoid X Receptor (RXR) Library
  4. Peroxisome Proliferator-Activated Receptor (PPAR) Library
  5. Circadian Rhythm Modulator Library
  1. Calorie Restriction Mimetic Library
  2. Growth Hormone/IGF-1 Pathway Library
  3. Antioxidant Response Element (ARE) Library
  4. Telomerase Modulator Library
  5. Proteostasis Library
  1. Insulin Sensitizer Library
  2. Adiponectin Receptor Library
  3. Ghrelin/Leptin Library
  4. Bile Acid Receptor (FXR/TGR5) Library
  5. Endoplasmic Reticulum (ER) Stress Library
  1. Heat Shock Protein (HSP) Inducer Library
  2. Lysosomal Function Library
  3. Metabolite-like Library (Endogenous mimicking)
  4. Glycation Inhibitor Library
  5. Stem Cell Modulator Library

Neurodegeneration & CNS

  1. Amyloid Aggregation Inhibitor Librar.
  2. Tau Protein Targeted Library
  3. Alpha-Synuclein Focused Library (Parkinson’s)
  4. Neuroinflammation Library (Microglia targeting)
  5. TREM2 Modulator Library
  6.  
  1. Acetylcholinesterase Inhibitor Library
  2. NMDA Receptor Library
  3. GABAergic Library
  4. Dopaminergic Library
  5. Neurotrophic Factor Mimetic Library (BDNF/NGF)
  1. Sigma Receptor Library
  2. LRRK2 Inhibitor Library (Genetic Parkinson’s)
  3. GBA (Glucocerebrosidase) Library
  4. Monoamine Oxidase (MAO) Library
  5. Nrf2 Activator Library (Neuroprotection)
  1. Blood-Brain Barrier Shuttle Library (For drug delivery)
  2. Microglial Phagocytosis Library
  3. Astrogliosis Modulator Library
  4. Exosome Modulator Library
  5. Synaptic Plasticity Library
  1. Myelin Repair/Remyelination Library
  2. Trk Receptor Library
  3. Purinergic Receptor (P2X7) Library
  4. Kynurenine Pathway Library
  5. Oligonucleotide Delivery Ligand Library (For CNS gene therapy)

Targeted Protein Degradation (TPD) & Proximity

  1. PROTAC Linker Library (Different chain lengths for E3 recruitment)
  2. Cereblon (CRBN) Focused Library (The most common E3 ligase target)
  3. VHL Ligand Library (Von Hippel-Lindau recruitment)
  4. IAP Ligand Library (Inhibitor of Apoptosis proteins)
  5. MDM2 Degrater Library (Specifically for p53 stabilization)
  1. Molecular Glue Degrader Set (For proteins without binding pockets)
  2. LYTAC (Lysosome-Targeting) Library (Degrading extracellular proteins)
  3. AUTAC (Autophagy-Targeting) Library (Degrading organelles/aggregates)
  4. E3 Ligase Screening Set (Identifying new “hijackable” ligases)
  5. Bifunctional Small Molecule Library (For induced proximity)
  1. DCAF15 Focused Library (A novel E3 ligase target)
  2. TRIM24 Targeted Library (Oncogenic transcriptional co-regulator)
  3. Ubiquitin Specific Protease (USP) Library (Deubiquitinase inhibitors)
  4. Deubiquitinase (DUB) Targeted Set
  5. E1/E2 Enzyme Inhibitor Library
  1. Proteasome Modulator Library
  2. NEDD8 Pathway Library
  3. Covalent E3 Recruiter Library
  4. Small Molecule Chimeras Library
  5. HaloTag/SNAP-tag Ligand Library (For experimental degradation)
  1. Degrader-Drug Conjugate (DDC) Library
  2. Targeted Protein Stabilization (DUBTAC) Library
  3. RNA-Targeted Degradation Library
  4. Phosphorylation-Inducing Chimeras (PHICS) Library
  5. Aggrephagy-Inducing Library (For neurodegenerative plaques)

Rare & Orphan Diseases

  1. Cystic Fibrosis (CFTR) Corrector Library
  2. Duchenne Muscular Dystrophy (DMD) Splicing Library
  3. Lysosomal Storage Disorder (LSD) Library
  4. Huntingtin (HTT) Protein Modulator Library
  5. Spinal Muscular Atrophy (SMA) SMN2 Library
  1. Amyotrophic Lateral Sclerosis (ALS) SOD1 Library
  2. Fragile X Syndrome Library
  3. Sickle Cell Disease HbF Inducer Library
  4. Phenylketonuria (PKU) Metabolic Library

135. Gaucher Disease Chaperone Library

  1. Fabry Disease Focused Set
  2. Wilson Disease Copper Chelator Library
  3. Hereditary Angioedema (HAE) Library
  4. Fibrodysplasia Ossificans Progressiva (FOP) Library
  5. Niemann-Pick Type C (NPC) Library
  1. Retinitis Pigmentosa Library
  2. Batten Disease Library
  3. Tay-Sachs Disease Library
  4. Achondroplasia (FGFR3) Library
  5. Progeria (LMNA) Focused Library
  1. Pompe Disease Enzyme Enhancer Library
  2. Primary Ciliary Dyskinesia Library
  3. Osteogenesis Imperfecta Library
  4. Alkaptonuria Focused Library
  5. Rare Pediatric Oncology Library (DIPG, Neuroblastoma)

Transcription Factors & RNA (151–175)

  1. MYC-MAX Interaction Inhibitor Library
  2. HIF-1alpha/HIF-2alpha Library
  3. SOX2 Focused Library (Stemness maintenance in cancer)
  4. GATA Transcription Factor Library
  5. p53 Re-activator Library
  1. FOXM1 Targeted Library
  2. Androgen Receptor Splice Variant (AR-V7) Library
  3. Nuclear Factor Kappa B (NF-kB) Library
  4. STAT3/STAT5 Phosphorylation Library
  5. AP-1 Transcription Factor Library
  1. Zinc Finger Targeted Library
  2. Leucine Zipper Interaction Library
  3. Helix-Loop-Helix (HLH) Library
  4. RNA G-Quadruplex Stabilizer Library
  5. microRNA (miRNA) Modulator Library
  1. IncRNA (Long non-coding RNA) Library
  2. Riboswitch Targeted Library
  3. Spliceosome Inhibitor Library
  4. RNA Decoy Library
  5. Translation Initiation (eIF4E) Library
  1. N6-methyladenosine (m6A) Modulator Library
  2. RNA Polymerase II/III Library
  3. TATA-Binding Protein (TBP) Library
  4. CREB/CBP Interaction Library
  5. E2F Transcription Factor Library

Immuno-Oncology & "Hard-to-Hit" Mechanisms

  1. STING Agonist Library (Cold-to-hot tumor conversion)
  2. cGAS Inhibitor Library (Autoimmunity/Oncology)
  3. IDO1/TDO Targeted Library
  4. Adenosine A2A/A2B Receptor Library
  5. VISTA/LAG3/TIM3 Small Molecule Library
  1. Toll-Like Receptor (TLR) 7/8/9 Library
  2. NLRP3 Inflammasome Library
  3. Exosome Secretion Inhibitor Library
  4. CD47-SIRPalpha Interaction Library
  5. PD-L1 Small Molecule Inhibitor Library (Not antibodies)
  1. Cytokine Receptor Fragment Library
  2. Complement System (C3/C5) Library
  3. Macrophage Polarization Library
  4. Natural Killer (NK) Cell Activator Library
  5. Chemokine (CCR/CXCR) Library
  1. FGF/FGFR Pathway Library
  2. Hedgehog (Shh) Pathway Library
  3. Notch Signaling Library
  4. Hippo Pathway (YAP/TAZ) Library
  5. TGF-beta Receptor Library
  1. Paraptosis/Methuosis Inducer Library
  2. Gold-Standard Reference Set (Known bioactives)
  3. Diversity-Oriented Synthesis (DOS) Library
  4. Spatially Defined Macrocycle Library
  5. AI-Designed “Novel Scaffold” Library (100% synthetic novelty)