Small Molecules: An Introduction

What are Small Molecules?
Small molecules have been the cornerstone for drug development and discovery for the past century. Although the number of marketed biologics has sharply increased,1 most marketed pharmaceuticals are small molecules. Before technological advances enabled high-throughput screening and combinatorial chemistry, small molecules were extracted from natural substances. Salicin, first manufactured into pills by Joseph Buchner in 1828, was derived from willow bark which the Egyptians and Sumerians used for pain relief as early as 3000 years BC. Other chemists derived salicin from the meadowsweet flower. This formulation evolved to become a small molecule still used in 700 to 1,000 clinical trials per year and is better known by its common name, Aspirin. 2 Small molecules for pain relief have evolved considerably, and diverged into several classes that comprise the bulk of marketed pain relief products:

  • Non-steroidal anti-inflammatory drugs (NSAIDs) (e.g., ibuprofen, naproxen, indomethacin, diclofenac, ketoprofen)
  • COX-2 inhibitors (e.g., celecoxib)
  • Opioids (e.g., buprenorphine, codeine, hydrocodone, methadone, morphine, hydromorphone, oxycodone, meperidine, pentazocine)
  • Central analgesics (e.g., tramadol)
  • Topical analgesics (e.g., capsaicin)
  • Topical anesthetics (e.g., benzocaine, dibucaine, lidocaine)

Typically weighing < 1000 daltons, their size enables small molecules to be easily manufactured into pills for oral administration and readily absorbed following gastrointestinal dissolution. Most orally active compounds that have achieved Phase II status follow the Rule of Five: ≤ 500 daltons; log P ≤ 5; H-bond donors ≤ 5; H-bond acceptors ≤ 10.3 More than 10 rotatable bonds correlates with reduced bioavailablility.4 Small molecules that act within the central nervous system possess a polar surface area ≤ 60 – 70.5 Additionally, if the sum of the nitrogen and oxygen atoms is ≤ 5, there is high probability that the small molecule will cross the blood-brain barrier.6

Small molecules facilitate research discovery in many fields of study including:

  • Apoptosis
  • Cell Signaling
  • Ion Channels and Transporters
  • Heat Shock Proteins
  • Oxidative Stress

Brefeldin A, an intracellular transport inhibitor, was first discovered as a potential antiviral agent. However, this fungal natural product also enables high temporal control of membrane trafficking and thus has been extensively used as a small molecule probe.7

Small molecules, once valued as therapeutic agents, have recently gained new importance by providing insight into cellular mechanisms. Prazocin, a small molecule used extensively as an anti-hypertensive agent in the late 20th century, has been shown to uniquely impact the sorting step during endocytic trafficking.8 This discovery has generated new interest in prazocin as a high-quality probe.9

Colchicine, derived from the autumn crocus (Colchicum autumnale) has anti-inflammatory properties and is FDA-approved to treat gout.10 However, colchicine has been used extensively as an R & D probe because it alters the polymerization of primary cytoskeletal structural components.11

Small molecules differ in important ways from other types of drug compounds (e.g., proteins, or biologics). For example, small molecules developed for oncology therapies penetrate the cell wall and target the inside of the cell.12 Once inside, the small molecule can fight cancer by inducing cell death13,14 and modulating transcription factors.15

Small molecules used in oncology include diverse agents with varied mechanisms of action:

  • Alkylating agents
    • Nitrogen mustards (e.g., mechlorethamine, chlorambucil, cyclophosphamide, ifosfamide, melphalan)
    • Alkyl sulfonates (e.g., busulfan)
    • Nitrosoureas (e.g., streptozotocin, carmustine [BCNU], lomustine)
    • Triazines (e.g., dacarbazine [DTIC], temozolomide)
    • Ethylenimines (e.g., thiotepa, altretamine [hexamethylmelamine])
    • Platinum (e.g., cisplatin, carboplatin, oxyplatin)
  • Antimetabolites (e.g., 5-fluorouracil [5-FU], 6-mercaptopurine [6-MP], capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine, hydroxyurea, pemetrexed)
  • Anthracyclines (e.g., daunorubicin, doxorubicin, epirubicin, idarubicin)
  • Anti-tumor antibiotics (e.g., actinomycin-D, bleomycin, mitomycin-C, anisomycin, geldanamycin, 17-DMAG, 17-AAG)
  • Topoisomerase inhibitors (e.g., Mitoxantrone, topotecan, irinotecan [CPT-11], etoposide [VP-16], Teniposide, camptothecin)
  • Mitotic inhibitors
    • Taxanes (e.g., paclitaxel, docetaxel, taxol)
    • Epothilones (e.g., ixabepilone)
    • Vinca alkaloids (e.g., vinblastine, vincristine, vinorelbine)
    • Estramustine
  • Corticosteroids (e.g., prednisone, methylprednisone, dexamethasone)
  • Proteosome inhibitors (e.g., bortezomib, carflizomib, aclacinomycin A, D)
  • Immunomodulators (e.g., thalidomide, lenalidomide, pomalidomide)

The ability to enter the cell has enabled cancer treatments to evolve from the broad application of cytotoxic chemotherapy, to personalized medicine that exploits the genetic vulnerabilities of the tumor.16

When compared to biologics, the structure of a small molecule is relatively simple.17 The active substances in biologics comprise large protein isoforms, in contrast to the single molecular entities that generally make up small molecules.18 It is likely therefore that the active substances are identical between two biologic products.19 Small molecules also require a less complex manufacturing process including20:

  • Fewer batch records (< 10 vs > 250)
  • Fewer quality tests (< 100 vs > 2,000)
  • Fewer critical process steps (< 100 vs >5,000)
  • More process data entries (< 4,000 vs > 60,000)

Modern medicine owes much of its progress toward disease treatments and cures to the development of small molecules. Small molecule synthesis continues to be a viable pathway to drug discovery and development for novel and generic products.