Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open-source biomolecular MD simulation software recognized for its efficiency, accuracy, and extensive range of simulation options. However, the complexity of setting up, running, and analyzing MD simulations for diverse systems often poses a significant challenge, requiring considerable time, effort, and expertise. Here, we introduce CHAPERONg, a tool that automates the GROMACS MD simulation pipelines for protein and protein-ligand systems. CHAPERONg also integrates seamlessly with GROMACS modules and third-party tools to provide comprehensive analyses of MD simulation trajectories, offering up to 20 post-simulation processing and trajectory analyses. It also streamlines and automates established pipelines for conducting and analyzing biased MD simulations via the steered MD-umbrella sampling workflow. Thus, CHAPERONg makes MD simulations more accessible to beginner GROMACS users whilst empowering experts to focus on data interpretation and other less programmable aspects of MD simulation workflows. CHAPERONg is written in Bash and Python, and the source code is freely available at https://github.com/abeebyekeen/CHAPERONg. Detailed documentation and tutorials are available online at dedicated web pages accessible via https://abeebyekeen.com/chaperong-online.

In recent times, researchers have explored food derived peptides to circumvent the side effects of synthetic drugs. This study therefore examined the amino acid constituents, in vitro antioxidant activities, angiotensin-1-converting enzyme (ACE), α-glucosidase and α-amylase inhibition kinetics of protein hydrolysate obtained from the seed of Luffa cylindrica. The peptide yield by pepsin (16.93 ± 0.28%) and trypsin (13.20 ± 1.02%) were significantly lower than that of Alcalase (34.04 ± 1.96%). Alcalase hydrolysate however displayed the highest ferric reducing antioxidant capacity (FRAC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) and H2O2 scavenging activities (0.63%, 85.88% and 41.69% respectively), while the highest superoxide scavenging activity was shown by peptic hydrolysate (57.89%). The ACE inhibition by the hydrolysates with IC50 of 0.32-0.93 mg/mL, increased as the concentration of the peptic hydrolysate increased with the highest ACE-inhibitory activity (74.99 ± 0.43%) at 1.2 mg/mL of peptic hydrolysate. Tryptic and Alcalase hydrloysates exhibited a strong α-amylase inhibition having 27.96 ± 0.06% and 36.36 ± 0.71% inhibitory capacity respectively with IC50 of 1.02-3.31 mg/mL. Alcalase hydrolysates demonstrated the strongest inhibition (65.81 ± 1.95%), followed by tryptic hydrolysates (54.53 ± 0.52%) in a concentration-dependent inhibition of α-glucosidase (IC50 , 0.48-0.80 mg/mL). Kinetic analysis showed that ACE-inhibition by different concentrations of Alcalase, pepsin and trypsin hydrolysates is uncompetitive, mixed-type and non-competitive respectively. α-Amylase was non-competitively inhibited while α-glucosidase was un-competitively inhibited by all the hydrolysates. The total amino acid concentration for Alcalase, trypsin and pepsin hydrolysates was 53.51g/100g, 75.40g/100g and 85.42g/100g of Luffa cylindrica seed protein hydrolysate respectively, with glutamate being the most concentrated essential amino acid in all the three hydrolysates. From these results, it can be deduced that Luffa cylindrica seed Alcalase and tryptic protein hydrolysates may play critical and indispensible role as bio-tools in diabetes and hypertension treatment.

Neem (Azadirachta indica) seed protein hydrolysates were investigated for in vitro antioxidant and angiotensin 1-converting enzyme (ACE)-inhibitory activities. Neem seed proteins were hydrolysed using pepsin, trypsin and Alcalase. The degree of pepsin hydrolysis of neem seed protein was significantly higher (p < 0.05) than those of trypsin and Alcalase hydrolysis. Proteolytic hydrolysis of the isolate resulted in hydrolysates with improved Arg/Lys ratio, with pepsin hydrolysates still being able to maintain an acceptable level of essential amino acids comparable to that of the isolate. At 2.5 mg/mL, pepsin neem seed protein hydrolysate (NSPH) demonstrated the strongest antioxidant activity with 67.15 % and 50.07 % DPPH- and superoxide anion radical-scavenging activities, respectively, while trypsin NSPH had the highest ferric-reducing power. Using N-[3-(2-furyl)acryloyl]-L-phenylalanyl-glycyl-glycine (FAPGG) as substrate, NSPHs strongly inhibited ACE (69.20-80.39 %) in a concentration-dependent manner. Pepsin NSPH had higher ACE-inhibitory activity than trypsin and Alcalase NSPHs. Kinetic studies showed the mechanism of ACE inhibition to be mixed-type with Ki values of 0.62, 0.84, 1.5 for pepsin, trypsin and alcalase NSPH, respectively. These results suggest that NSPH can be used as a potential nutraceutical with antioxidant capacity and inhibitory activity against ACE.

This study investigated the in vitro antihypertensive, antiradical and hydrogen peroxidescavenging properties of protein hydrolysates from Citrullus lanatus (watermelon) seed (CSPHs) obtained through enzymatic digestion. Proteins from watermelon seeds were isolated and enzymatically hydrolyzed with non-specific (alcalase), moderately specific (pepsin) and highly specific (trypsin) proteases, mimicking human gastrointestinal digestion. The hydrolysates were investigated for inhibitory property against angiotensin-I-converting enzyme (ACE) activity. Using N-[3-(2furyl)acryloyl]-L-phenylalanyl-glycyl-glycine as the substrate, CSPHs showed concentration-dependent ACE inhibition (IC 50 1.377-1.757 mg/mL) with peptic CSPH having the strongest ACE-inhibition followed by tryptic CSPH. Kinetic analysis revealed that peptic CSPH inhibited ACE activity in a mixedtype inhibition pattern while alcalase and tryptic CSPHs exhibited non-competitive inhibition mode. Peptic CSPH demonstrated the strongest DPPH radical-scavenging activity while tryptic CSPH showed the highest H 2 O 2-scavenging property. These results show that protein hydrolysates from watermelon seed possess bioactivities that could be exploited in the management of hypertension.

Several novel functional peptides have been successfully extracted from plant storage proteins. This study investigated the degree of hydrolysis, peptide yield, amino acid constituents, angiotensin converting enzyme (ACE), alpha amylase inhibitory and in vitro antioxidant activities of cashew (Anarcardium occidentale) nut proteins (CNP) hydrolysates (CNPHs). Cashew nut proteins (albumin and globulin) were hydrolysed using pancreatin, Alcalase and trypsin. The peptide yield and degree of hydrolysis (DH) of CNP by pancreatin (75.69 ± 0.84%; 37.39 ± 0.31) was significantly higher than those by Alcalase (61.67 ± 0.55%; 23.87 ± 0.23) and trypsin (43.33 ± 0.45%; 11 ± 0.15). The inhibition of ACE by albumin and globulin hydrolysates was concentration dependent. At 1.2 mg/mL, ACE-inhibitory activity of pancreatic cashew nut globulin (CNGH) hydrolysate (51.65 ± 1.2%) was significantly higher than those of Alcalase (34.603 ± 0.65%) and tryptic (29.92 ± 0.73%) CNGHs. Cashew nut albumin hydrolysate (CNAH) demonstrated concentration-dependent alpha-amylase inhibition (IC50 0.17 ± 0.02–0.41 ± 0.021 mg/mL). The order of inhibition was tryptic > Alcalase > pancreatic CNAHs. The pancreatic hydrolysates of both albumin and globulin fractions displayed the highest DPPH antioxidant activity, while pancreatic CNAH was the most potent superoxide anion scavenger. These findings therefore posit that cashew nut globulin and albumin hydrolysates are laden with useful bioactive peptides that may be further explored for regulation of blood pressure and sugar in hypertensive and diabetic in vivo models.