The Myxomavirus-derived protein Serp-1 has potent anti-inflammatory activity in models of vasculitis, lupus, viral sepsis, and transplant. Serp-1 has also been tested successfully in a Phase IIa clinical trial in unstable angina, representing a 'first-in-class' therapeutic. Recently, peptides derived from the reactive center loop (RCL) have been developed as stand-alone therapeutics for reducing vasculitis and improving survival in MHV68-infected mice. However, both Serp-1 and the RCL peptides lose activity in MHV68-infected mice after antibiotic suppression of intestinal microbiota. Here, we utilize a structure-guided approach to design and test a series of next generation RCL peptides with improved therapeutic potential that is not reduced when combined with antibiotic treatments. The crystal structure of the cleaved Serp-1 was determined to 2.5 Å resolution, and reveals a classical serpin structure with potential for serpin-derived RCL peptides to bind and inhibit mammalian serpins, plasminogen activator inhibitor 1 (PAI-1), anti-thrombin III (ATIII) and alpha-1 antitrypsin (A1AT) and target proteases. Using in silico modeling of Serp-1 RCL peptide, S-7, we designed several modified RCL peptides that were predicted to have stronger interactions with human serpins due to a higher number of stabilizing hydrogen bonds. Two of these peptides (MPS7-8 and -9) displayed extended activity, improving survival where activity was previously lost in antibiotic treated MHV68-infected mice (P < 0.0001). Mass spectrometry and kinetic assays suggest peptide interaction with ATIII, A1AT, and target proteases in mouse and human plasma. In summary, we present the next step towards the development of a promising new class of anti-inflammatory serpin-based therapeutic.