Biology subjects

Alfonso, A. R.

Publications and source records attributed to Alfonso, A. R..

3 recordsLinked to original sources

bioRxiv2026

APP and APLP2 Kunitz Domains Are Potent Endogenous Inhibitors of TMPRSS2 and Respiratory Virus Infection

Respiratory viruses depend on host proteases for activation of viral fusion proteins, making these enzymes attractive targets for broad-spectrum antiviral strategies. We previously identified Trypstatin, a human Bikunin-derived Kunitz domain, as a potent endogenous inhibitor of the airway serine protease TMPRSS2. Here, we investigated whether TMPRSS2 inhibition is shared by additional human Kunitz domains. Kunitz domains with high sequence similarity to Trypstatin were synthesized, refolded, and functionally characterized. Domains derived from amyloid precursor protein (APP) and amyloid precursor-like protein 2 (APLP2) potently inhibited TMPRSS2, with APP displaying subnanomolar activity comparable to camostat mesylate. APP and APLP2 selectively blocked SARS-CoV-2 Spike-mediated entry without affecting VSV-G-mediated entry or cell viability and inhibited infection by multiple coronaviruses and influenza viruses, but not TMPRSS2-independent rhinovirus. In primary human airway epithelial cultures, APP and Trypstatin reduced replication of SARS-CoV-2, endemic coronaviruses, and influenza A virus, and remained stable in airway mucus. These findings identify APP and APLP2 Kunitz domains as potent endogenous inhibitors of TMPRSS2-dependent respiratory virus infection and promising scaffolds for host-directed broad-spectrum antivirals.

microbiology↗

bioRxiv2025

ReaxFF-guided Optimisation of VIRIP-based HIV-1 Entry Inhibitors

Peptides hold great promise for safe and effective treatment of viral infections. However, their use is often constrained by limited efficacy and high production costs, especially for long or complex peptide chains. Here, we used ReaxFF molecular dynamics (MD) simulations to optimize the size and activity of VIRIP (Virus Inhibitory Peptide), a naturally occurring 20-residue fragment of 1-antitrypsin that binds the HIV-1 GP41 fusion peptide (FP), thereby blocking viral fusion and entry into host cells. Specifically, we used the NMR structure of the complex between an optimized VIRIP derivative (VIR-165) and the HIV-1 gp41 FP for ReaxFF-guided in silico analysis, evaluating the contribution of each amino acid in the interaction of the inhibitor with its viral target. This approach allowed us to reduce the size of the HIV-1 FP inhibitor from 20 to 10 amino acids (2.28 to 1.11 kDa). HIV-1 infection assays showed that the size-optimized VIRIP derivative (soVIRIP) retains its broad-spectrum anti-HIV-1 capability and is non-toxic in the vertebrate zebrafish model. Compared to the original VIRIP, soVIRIP displayed more than 100-fold higher antiviral activity (IC50 of [~]120 nM). Thus, it is more potent than a dimeric 20-residue VIRIP derivative (VIR-576) that was proven safe and effective in a phase I/II clinical trial. Our results show that ReaxFF-based MD simulations represent a suitable approach for the optimization of therapeutic peptides.

molecular biology↗

bioRxiv2022

Evolution of a Plastic Surgery Summer Research Program

BackgroundEarly surgical exposure and research fellowships have been independently shown to influence medical students specialty choice, increase academic productivity, and impact residency match. However, to our knowledge there is no published guidance on the implementation of formal plastic surgery summer research programs for first year medical students. We present our institutional experience developing a plastic surgery summer research program over seven years (2013-2020) in an effort to inform program development at other institutions. We hypothesized that this early, formal exposure could spark interest in pursuing research activities throughout medical school and residency. MethodsFrom 2013 to 2016, a sole basic science research arm existed. In 2017, a clinical research arm was introduced, with several supplemental activities including structured surgical skills sessions. A formalized selection process was instituted in 2014. Participant feedback was analyzed on a yearly basis. Long-term outcomes included continued research commitment, productivity, and residency match. ResultsThe applicant pool has reached 96 applicants in 2019, with 85% from outside institutions. Acceptance rate reached 7% in 2020. With adherence to a scoring rubric for applicant evaluation, good to excellent interrater reliability was achieved (ICC = 0.75). Long-term outcomes showed that on average per year, 28% of participants continued departmental research activities and 29% returned for dedicated research. Upon finishing medical school, participants had a mean of 6.9{+/-}4.0 peer-reviewed publications. 62% of participants matched into a surgical residency program, with 54% in integrated plastic surgery. ConclusionsA research program designed for first year medical students interested in plastic surgery can achieve academic goals. Students are provided with mentorship, networking opportunities, and tools for self-guided learning and career development.

scientific communication and education↗