Journal
CHEMICAL BIOLOGY & DRUG DESIGN
Volume 79, Issue 5, Pages 703-718Publisher
WILEY
DOI: 10.1111/j.1747-0285.2012.01324.x
Keywords
complement system; C3; mechanism-based drug design; molecular modeling; compstatin; structure-based drug design
Funding
- Cyprus Fulbright Commission
- Cyprus Research Promotion Foundation [INFRASTRUCTURE/STRATEGIC/0308/31]
- European Regional Development fund
- University of Cyprus
- DoD
- Air Force Office of Scientific Research
- National Defense Science and Engineering Graduate (NDSEG) [32 CFR 168a]
- National Institutes of Health [5R01GM052032]
- Beckman Initiative for Macular Degeneration [1112]
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We report the computational and rational design of new generations of potential peptide-based inhibitors of the complement protein C3 from the compstatin family. The binding efficacy of the peptides is tested by extensive molecular dynamics-based structural and physicochemical analysis, using 32 atomic detail trajectories in explicit water for 22 peptides bound to human, rat or mouse target protein C3, with a total of 257 ns. The criteria for the new design are: (i) optimization for C3 affinity and for the balance between hydrophobicity and polarity to improve solubility compared to known compstatin analogs; and (ii) development of dual specificity, human-rat/mouse C3 inhibitors, which could be used in animal disease models. Three of the new analogs are analyzed in more detail as they possess strong and novel binding characteristics and are promising candidates for further optimization. This work paves the way for the development of an improved therapeutic for age-related macular degeneration, and other complement system-mediated diseases, compared to known compstatin variants.
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