PepDRED: De Novo Peptide Design with Strong Binding Affinity for Target Protein.

De novo design of peptides that bind specifically to functional proteins is beneficial for diagnostics and therapeutics. However, complex permutations and combinations of amino acids pose significant challenges to the rational design of peptides with desirable stability and affinity. Herein, we develop a computational-based evolution method, namely, peptidomimetics-driven recognition elements design (PepDRED), to derive hemoglobin-inspired peptidomimetics. PepDRED mimics the natural evolutionism pipeline to generate stable apovariant (AVs) structures for wild-type counterparts via automated point mutations and validates their efficiency through free binding energy analysis and per residue energy decomposition analysis. For application demonstration, we applied PepDRED to design de novo peptides to bind FhuA, a typical TonB-dependent transporter (TBDT). TBDTs are Gram-negative bacterial outer membrane proteins responsible for iron transport and vital for bacterial resistance. PepDRED generated a pool of AVs and proceeded to reach an optimized peptide, AV440, with a remarkable binding affinity of -21 kcal/mol. AV440 is ∼2.5-fold stronger than the existing FhuA inhibitor Microcin J25. Network energy analysis further unveils that incorporating methionine (M42) in the N-terminal region significantly enhances inter-residue contacts and binding affinity. PepDRED offers a prompt and efficient in silico approach to develop potent peptide candidates for target proteins.

Melamine detection in liquid milk based on selective porous polymer monolith mediated with gold nanospheres by using surface enhanced Raman scattering.

A rapid and fast detection of trace amounts of melamine in milk is reported by using Gold Nano Spheres embedded monolith conjugates. Monolith was synthesized by the polymerization of Glycidyl Methacrylate (GMA) and Ethylene Dimethacrylate(EDMA) (cross linker and functional monomer), Cyclohexanol (Porogen formation) and 2, 2-Dimethoxy-2-phenyl-acetophenone (photo-initiator) on gold coated silicon wafer. In order to gauge the influence of monolith on SERS signal activity, three shapes of gold nanoparticles namely Gold Nano Spheres (GNSs), Gold Nanorods (GNRs) and Triangular Gold Nanoprisms (GNPrs) were immobilized on monolithic surface and analyzed by the signal molecule Rhodamine (R6G). The Raman Enhancement efficiency of the above three shapes incorporated with monolith was monitored by calculating their maximum enhancement factors. Among three morphologies, Gold Nano Spheres integrated in GMA-EDMA Monolith Sensor (GNS@GEMS) was found more effective for detection of R6G than two others and was therefore projected in analysis of melamine sensing in commercial milk. A linear relationship of regression model (R2 = 0.99) was observed between melamine SERS intensity (at 710 cm-1) and varied concentrations (6.5 < mg/L < 0.125). The lower limit of detection (LOD) and limit of quantification (LOQ) for melamine was determined 0.11 mg/L and 0.38 mg/L respectively. The time window for detection of melamine was 10 min and hence our method is compatible with the FDA's tolerance limit in USA and China (1 mg/L).