Targeting species specific amino acid residues: Design, synthesis and biological evaluation of 6-substituted pyrrolo[2,3-d]pyrimidines as dihydrofolate reductase inhibitors and potential anti-opportunistic infection agents

Bioorg Med Chem. 2018 May 15;26(9):2640-2650. doi: 10.1016/j.bmc.2018.04.032. Epub 2018 Apr 17.


To combine the potency of trimetrexate (TMQ) or piritrexim (PTX) with the species selectivity of trimethoprim (TMP), target based design was carried out with the X-ray crystal structure of human dihydrofolate reductase (hDHFR) and the homology model of Pneumocystis jirovecii DHFR (pjDHFR). Using variation of amino acids such as Met33/Phe31 (in pjDHFR/hDHFR) that affect the binding of inhibitors due to their distinct positive or negative steric effect at the active binding site of the inhibitor, we designed a series of substituted-pyrrolo[2,3-d]pyrimidines. The best analogs displayed better potency (IC50) than PTX and high selectivity for pjDHFR versus hDHFR, with 4 exhibiting a selectivity for pjDHFR of 24-fold.

Keywords: DHFR inhibitors; Opportunistic infections; Pneumocystis pneumonia; Pyrrolo[2,3-d]pyrimidines; hDHFR; pjDHFR.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acids / chemistry*
  • Anti-Bacterial Agents / chemical synthesis
  • Anti-Bacterial Agents / pharmacology*
  • Catalytic Domain
  • Crystallography, X-Ray
  • Drug Design
  • Enzyme Assays
  • Folic Acid Antagonists / chemical synthesis
  • Folic Acid Antagonists / chemistry
  • Folic Acid Antagonists / metabolism
  • Folic Acid Antagonists / pharmacology*
  • Humans
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Docking Simulation
  • Molecular Structure
  • Pneumocystis carinii / enzymology
  • Protein Binding
  • Pyrimidines / chemical synthesis
  • Pyrimidines / chemistry
  • Pyrimidines / metabolism
  • Pyrimidines / pharmacology*
  • Pyrroles / chemical synthesis
  • Pyrroles / chemistry
  • Pyrroles / metabolism
  • Pyrroles / pharmacology*
  • Sequence Homology, Amino Acid
  • Species Specificity
  • Tetrahydrofolate Dehydrogenase / chemistry
  • Tetrahydrofolate Dehydrogenase / metabolism


  • Amino Acids
  • Anti-Bacterial Agents
  • Folic Acid Antagonists
  • Pyrimidines
  • Pyrroles
  • Tetrahydrofolate Dehydrogenase