Structure-based approaches to antibiotic drug discovery

Tecoma stans: Alkaloid Profile and Antimicrobial Activity

AIM

Tecoma stans (L.) Kunth is a promising species in the trumpet creeper family Bignoniaceae. This study aimed at showing the antibacterial and antifungal potentials of T. stans methanolic leaf extract (TSME) correlated to its phytoconstituents.

MATERIALS AND METHODS

The antimicrobial potential of TSME was evaluated using agar diffusion method. The main alkaloids were separated on silica gel column and identified using nuclear magnetic resonance spectral analysis. Molecular docking was performed for the isolated compounds against MurD ligase, penicillin-binding protein, and dihydropteroate synthase enzyme to rationalize the observed antibacterial effect.

RESULTS AND DISCUSSION

TSME showed significant antibacterial effect against all tested microorganisms with comparable minimum inhibitory concentration (MIC) to the ampicillin and gentamicin with MIC values ranging between 0.98 and 1.95 µg/mL, in addition to a promising antifungal effect when compared to amphotericin with MIC values 3.9 and 15.63 µg/mL for Aspergillus flavus and Candida albicans, respectively. Several alkaloids were separated, purified, and identified as tecostanine, 4-OH tecomanine, 5-hydroxyskytanthine, and tecomanine, which were previously isolated from T. stans. The docking study showed that the alkaloids bind in a similar fashion to the co-crystallized ligands of the crystal structures of MurD ligase. The binding poses and scores in the case of penicillin-binding protein and dihydropteroate synthase did not match the co-crystallized ligands in their crystal structures. The in silico results suggest an antibacterial mechanism that involves the inhibition of MurD ligase.

CONCLUSION

T. stans alkaloids could represent the basic skeleton for a powerful antimicrobial agent.

A rational free energy-based approach to understanding and targeting disease-causing missense mutations

BACKGROUND AND SIGNIFICANCE

Intellectual disability is a condition characterized by significant limitations in cognitive abilities and social/behavioral adaptive skills and is an important reason for pediatric, neurologic, and genetic referrals. Approximately 10% of protein-encoding genes on the X chromosome are implicated in intellectual disability, and the corresponding intellectual disability is termed X-linked ID (XLID). Although few mutations and a small number of families have been identified and XLID is rare, collectively the impact of XLID is significant because patients usually are unable to fully participate in society.

OBJECTIVE

To reveal the molecular mechanisms of various intellectual disabilities and to suggest small molecules which by binding to the malfunctioning protein can reduce unwanted effects.

METHODS

Using various in silico methods we reveal the molecular mechanism of XLID in cases involving proteins with known 3D structure. The 3D structures were used to predict the effect of disease-causing missense mutations on the folding free energy, conformational dynamics, hydrogen bond network and, if appropriate, protein-protein binding free energy.

RESULTS

It is shown that the vast majority of XLID mutation sites are outside the active pocket and are accessible from the water phase, thus providing the opportunity to alter their effect by binding appropriate small molecules in the vicinity of the mutation site.

CONCLUSIONS

This observation is used to demonstrate, computationally and experimentally, that a particular condition, Snyder-Robinson syndrome caused by the G56S spermine synthase mutation, might be ameliorated by small molecule binding.

The key role of genomics in modern vaccine and drug design for emerging infectious diseases

It can be argued that the arrival of the “genomics era” has significantly shifted the paradigm of vaccine and therapeutics development from microbiological to sequence-based approaches. Genome sequences provide a previously unattainable route to investigate the mechanisms that underpin pathogenesis. Genomics, transcriptomics, metabolomics, structural genomics, proteomics, and immunomics are being exploited to perfect the identification of targets, to design new vaccines and drugs, and to predict their effects in patients. Furthermore, human genomics and related studies are providing insights into aspects of host biology that are important in infectious disease. This ever-growing body of genomic data and new genome-based approaches will play a critical role in the future to enable timely development of vaccines and therapeutics to control emerging infectious diseases.