Structure-Based Design of a Potent and Selective Small Peptide Inhibitor of Mycobacterium tuberculosis 6-Hydroxymethyl-7, 8-Dihydropteroate Synthase: A Computer Modelling Approach

Antibacterial Effect of Sesame Protein-Derived Peptides against Escherichia coli and Staphylococcus aureus: In Silico and In Vitro Analysis

This study aimed to screen out antibacterial peptides derived from sesame (Sesamum indicum L.) through in silico and in vitro methods. In silico proteolysis of sesame proteins with pepsin, trypsin, and chymotrypsin was performed with the online server BIOPEP-UWM. The CAMPR3 online server was used to predict the antimicrobial effect of peptides. The ToxinPred, PepCalc, and AllergenFP tools were utilized to forecast the physicochemical properties, toxicity, and allergen of the peptides. Molecular docking analysis showed that six cationic antimicrobial peptides could directly interact with the key sites of dihydropteroate synthase, whereas Ala-Gly-Gly-Val-Pro-Arg and Ser-Thr-Ile-Arg exhibited the strongest binding affinity. In vitro antibacterial experiment showed the minimum inhibitory concentration (MIC) of Ser-Thr-Ile-Arg against Escherichia coli and Staphylococcus aureus was 1024 and 512 µg/mL, respectively. Meanwhile, MIC of Ala-Gly-Gly-Val-Pro-Arg against both bacterial species was 512 µg/mL. Our results suggest that peptides from sesame possess the ability to potentially hinder bacterial activity.

Protein targets in Mycobacterium tuberculosis and their inhibitors for therapeutic implications: A narrative review

Advancement in the area of anti-tubercular drug development has been full-fledged, yet, a very less number of drug molecules have reached phase II clinical trials, and therefore "End-TB" is still a global challenge. Inhibitors to specific metabolic pathways of Mycobacterium tuberculosis (Mtb) gain importance in strategizing anti-tuberculosis drug discovery. The lead compounds that target DNA replication, protein synthesis, cell wall biosynthesis, bacterial virulence and energy metabolism are emerging as potential chemotherapeutic options against Mtb growth and survival within the host. In recent times, the in silico approaches have become most promising tools in the identification of suitable inhibitors for specific protein targets of Mtb. An update in the fundamental understanding of these inhibitors and the mechanism of interaction may bring hope to future perspectives in novel drug development and delivery approaches. This review provides a collective impression of the small molecules with potential antimycobacterial activities and their target pathways in Mtb such as cell wall biosynthesis, DNA replication, transcription and translation, efflux pumps, antivirulence pathways and general metabolism. The mechanism of interaction of specific inhibitor with their respective protein targets has been discussed. The comprehensive knowledge of such an impactful area of research would essentially reflect in the discovery of novel drug molecules and effective delivery approaches. This narrative review encompasses the knowledge of emerging targets and promising n that could potentially translate in to the anti-TB-drug discovery.

Antimicrobial bioactive peptides from goat Milk proteins: In silico prediction and analysis

The main goal of this study was to assess the potential proteins of goat milk (i.e. α-s1-casein, α-s2-casein, β-casein, κ-casein, α-lactoglobulin and β-lactalbumin) as precursors of antimicrobial peptides (AMPs). Bioinformatics tools such as BIOPEP-UWM (enzyme action) were used for the in silico gastrointestinal digestion via a cocktail of pepsin, trypsin, and chymotrypsin A. The antimicrobial activity of peptides was predicted by using four algorithms, including Random Forest, Support Vector Machines, Artificial Neural Network and Discriminant Analysis on CAMPR3 online server, which works on Hidden Markov Models. Different online tools predicted the physiochemical properties, allergenicity, and toxicity of peptides as well. In silico gastrointestinal digestion simulation of proteins by enzymes cocktail yielded a total of 83 potential AMPs, with thirteen peptides being confident by all four algorithms. More AMPs were released from β-casein (21) than from β-lactoglobulin (16), α-s1-casein (15), α-s2-casein (12), κ-casein (11) and α-lactalbumin (9). A total of 17 peptides were cationic, and the majority of the peptides were extended AMPs. These peptides were released from α-s1-casein (SGK, IQK), α-s2-casein (SIR, AIH, TQPK), β-casein (GPVR, AVPQR, AIAR, GVPK, SQPK, PVPQK, IH, VPK), k-casein (AIPPK, QQR, IAK, TVPAK). All of the AMPs were anticipated to be non-toxic, and 54 of the 83 peptides were confirmed to be non-allergic, with the remaining 29 suspected of being allergenic and 31 to be predicted to have good water solubility. Further the molecular docking was used to evaluate the potent dihydropteroate synthase (DHPS) inhibitors. On the basis of ligand binding energy, 17 predicted AMPs were selected and then analyzed by AutoDock tools. Among the 17 AMPs, 3 AMPs were predicted as high-potent antimicrobial. Based on these findings, in silico investigations reveal that proteins of goat milk are a potential source of AMPs. These peptides can be synthesized and improved for use in the food sector. PRACTICAL APPLICATIONS: Goat milk is regarded as a high-quality milk protein source. According to this study, goat milk protein is a possible source of AMPs, and therefore, most important AMPs can be synthesized and developed for use in the food sector.

Curcumin rescue p53Y220C in BxPC-3 pancreatic adenocarcinomas cell line: Evidence-based on computational, biophysical, and in vivo studies

BACKGROUND

The p53, tumor suppressor protein is inactivated upon mutation in the DNA-binding domain and the non-functional protein leads to cancers. The p53Y220C is one of the most frequently observed mutations in p53 with a scope of rescuing the protein function using small molecules.

METHODS

Using computational modeling, biophysical, and experimental cell-based studies we tried to understand the molecular basis of Curcumin as a potential small molecule to stabilize p53Y220C mutant and restore its function. The pancreatic adenocarcinomas BxPC-3 p53Y220C mutant cell line was used for cell-based assays to determine the therapeutic potential of Curcumin to restore mutant p53 to function like wild type.

RESULTS

Our results showed that the Curcumin binds p53Y220C with K_d = 3.169 ± 0.257 μM and it increases the DNA binding affinity of the mutant by 4-fold with K_d = 851.29 ± 186.27 nM. By Fluorescence, CD, and IR spectroscopy, we could characterize the secondary structural changes and stabilization of the p53Y220C DNA binding domain upon Curcumin binding. By caspase-3 and Annexin V assays, we could demonstrate that Curcumin at 3 μM to 8 μM concentration could initiate p53 mediated apoptosis in BxPC-3 cell line. Based on our experimental studies, we propose a mechanism for the activation of ATM/Chk1 kinases pathways for apoptosis and/or G2/M cell cycle arrest in the BxPC-3 cell line mediated by functionally restored p53Y220C.

CONCLUSION

The study indicated that the natural compound Curcumin could rescue mutant p53Y220C in BxPC-3 pancreatic adenocarcinomas cell line to function like wild-type and activate apoptotic pathways.

Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies

All mRNAs cannot be translated into full-length proteins due to ribosome-stalling that leads to release of peptidyl-tRNA which can be lethal for bacterial survival. The enzyme peptidyl-tRNA hydrolase (PtH) hydrolyses the ester bond between nascent peptide and tRNA of peptidyl-tRNA and rescues the cells from toxicity. PtH is an essential enzyme in bacteria and inhibiting this crucial enzyme can serve to combat bacterial diseases. But due to lack of understanding about the catalytic mechanism of PtH, its inhibitors have not been developed. In this work, we have carried out the binding studies of M. tuberculosis and E. coli PtH with the peptidyl-tRNA analogue (puromycin) using ITC, FTIR, CD experiments followed by docking and MD simulations to identify the potential active site residues that would help to design PtH inhibitors. Binding studies of puromycin with both PtH by ITC experiments demonstrate similar thermodynamic parameters and three fold difference in their K_D. CD and FTIR studies detected changes in secondary structure composition of PtH in the presence of puromycin with different degree of perturbation. Though interactions with puromycin are conserved in both proteins, modelling studies revealed that water mediated interactions in M. tb-PtH resulting in higher affinity to puromycin.

The molecular mechanism involved in cardioprotection by the dietary flavonoid fisetin as an agonist of PPAR-γ in a murine model of myocardial infarction

The methodology exploring the cardioprotective potential of the flavonoid Fisetin through its ability to modulate PPAR-γ was unraveled in the present study. Computational modelling through molecular docking based binding study of interactions between Fiestin and PPAR-γ revealed the potential role of Fisetin as an agonist of PPAR-γ. A murine model of cardiac ischemia-reperfusion injury was used to explore this further. Male Wistar Rats were randomly assigned to five groups. Fisetin (20 mg/kg; p. o) was administered for 28 days. Ischemia was induced for 45 min on the 29th day followed by 60 min of reperfusion. Fisetin pretreatment upregulated the expression of PPAR-γ in heart tissue significantly Cardioprotection was assessed by measurement of hemodynamic parameters, infarct size, ELISA for oxidative stress, immunohistochemistry and TUNEL assay for apoptosis, and western blot analysis for MAPK proteins and inflammation. PPAR-γ activation by fisetin led to significantly reduced infarct size, suppression of oxidative stress, reduction of cardiac injury markers, alleviation of inflammation, and inhibition of apoptosis The MAPK-based molecular mechanism showed a rise in a key prosurvival kinase, ERK1/ERK2 and suppression of JNK and p38 proteins. The aforementioned beneficial findings of fisetin were reversed on the administration of a specific antagonist of PPAR-γ. In conclusion, through our experiments, we have proved that fisetin protects the heart against ischemia-reperfusion injury and the evident cardioprotection is PPAR-γ dependant. In conclusion, our study has revealed a prime mechanism involved in the cardioprotective effects of fisetin. Hence, Fisetin may be evaluated in further clinical studies as a cardioprotective agent in patients undergoing reperfusion interventions.

Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis

Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).

Protein-protein binding affinity prediction on a diverse set of structures

MOTIVATION

Accurate binding free energy functions for protein-protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities has allowed, for the first time, the evaluation and construction of binding free energy models using a diverse set of complexes, and a systematic assessment of our ability to model the energetics of conformational changes.

RESULTS

We construct a large set of molecular descriptors using commonly available tools, introducing the use of energetic factors associated with conformational changes and disorder to order transitions, as well as features calculated on structural ensembles. The descriptors are used to train and test a binding free energy model using a consensus of four machine learning algorithms, whose performance constitutes a significant improvement over the other state of the art empirical free energy functions tested. The internal workings of the learners show how the descriptors are used, illuminating the determinants of protein-protein binding.

AVAILABILITY

The molecular descriptor set and descriptor values for all complexes are available in the Supplementary Material. A web server for the learners and coordinates for the bound and unbound structures can be accessed from the website: http://bmm.cancerresearchuk.org/~Affinity.

CONTACT

paul.bates@cancer.org.uk.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.