Beyond the venom: Exploring the antimicrobial peptides from Androctonus species of scorpion.

Prevalent worldwide, the Androctonus scorpion genus contributes a vital role in scorpion envenoming. While diverse scorpionisms are observed because of several different species, their secretions to protect themselves have been identified as a potent source of antimicrobial peptide (AMP)-like compounds. Distinctly, the venom of these species contains around 24 different AMPs, with definite molecules studied for their therapeutic potential as antimicrobial, antifungal, antiproliferative and antiangiogenic agents. Our review focuses on the therapeutic potential of native and synthetic AMPs identified so far in the Androctonus scorpion genus, identifying research gaps in peptide therapeutics and guiding further investigations. Certain AMPs have demonstrated remarkable compatibility to be prescribed as anticancer drug to reduce cancer cell proliferation and serve as a potent antibiotic alternative. Besides, analyses were performed to explore the characteristics and affinities of peptides for membranes. Overall, the study of AMPs derived from the Androctonus scorpion genus provides valuable insights into their potential applications in medicine and drug development.

Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression.

BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for ß-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.

Identification of Dietary Bioflavonoids as Potential Inhibitors against KRAS G12D Mutant-Novel Insights from Computer-Aided Drug Discovery.

The KRAS G12D mutation is very frequent in many cancers, such as pancreatic, colon and lung, and has remained undruggable for the past three decades, due to its smooth surface and lack of suitable pockets. Recent small pieces of evidence suggest that targeting the switch I/II of KRAS G12D mutant could be an efficient strategy. Therefore, in the present study, we targeted the switch I (residues 25-40) and switch II (residues 57-76) regions of KRAS G12D with dietary bioflavonoids in comparison with the reference KRAS SI/II inhibitor BI-2852. Initially, we screened 925 bioflavonoids based on drug-likeness properties, and ADME properties and selected 514 bioflavonoids for further studies. Molecular docking resulted in four lead bioflavonoids, namely 5-Dehydroxyparatocarpin K (L1), Carpachromene (L2), Sanggenone H (L3), and Kuwanol C (L4) with binding affinities of 8.8 Kcal/mol, 8.64 Kcal/mol, 8.62 Kcal/mol, and 8.58 Kcal/mol, respectively, in comparison with BI-2852 (-8.59 Kcal/mol). Further steered-molecular dynamics, molecular-dynamics simulation, toxicity, and in silico cancer-cell-line cytotoxicity predictions significantly support these four lead bioflavonoids as potential inhibitors of KRAS G12D SI/SII inhibitors. We finally conclude that these four bioflavonoids have potential inhibitory activity against the KRAS G12D mutant, and are further to be studied in vitro and in vivo, to evaluate their therapeutic potential and the utility of these compounds against KRAS G12D mutated cancers.

Hydrogen bonds in anoplin peptides aid in identification of a structurally stable therapeutic drug scaffold.

Multi-drug resistance is a major issue faced by the global pharmaceutical industry. Short antimicrobial peptides such as anoplins can be used to replace antibiotics, thus mitigating this issue. Antimicrobial activity, non-toxicity, and structural stability are essential features of a therapeutic drug. Antimicrobial activity and toxicity to human erythrocytes have been previously reported for anoplin and anoplin R5K T8W. This study attempts to identify a therapeutic peptide drug scaffold between these peptides by examining their structural stability, mainly based on the hydrogen bonds (H-bond) found in their structures. The static structure of anoplin R5K T8W displayed lower H-bond distances than anoplin, thereby exhibiting enhanced structural stability. Dynamic stability studies revealed that conformers of anoplin R5K T8W exhibited lower hydrogen bond distances (HBDs), higher H-bond occupancies, and higher radial distribution function (RDF) of H-bonds in comparison with conformers of anoplin. Furthermore, conformers of anoplin R5K T8W generated using 50-ns molecular dynamics simulation displayed lower conformational free energy than anoplin, thus establishing its higher structural stability. Overall, anoplin R5K T8W can be claimed as a promising scaffold that may be used for therapeutic purposes. In conclusion, H-bonds play a major role in structural stability and may aid in identification of a therapeutic peptide scaffold. Graphical abstract.

Investigation of structural stability and functionality of homodimeric gramicidin towards peptide-based drug: a molecular simulation approach.

Increasing death rates due to antibiotic resistance deteriorate the existing treatment measures. Antimicrobial peptides have turned into the emerging cure for multidrug resistance. However, the stability and functionality determine an antimicrobial peptide as a drug. Analyses of the homodimeric ß-helical peptide, gramicidin have suggested the significant role of gramicidin-A, gramicidin-B, and gramicidin-C as antimicrobial compounds, but the structural basis for understanding the stability and functionality is insufficient to resolve multidrug resistance. To identify the best template among gramicidin types as a therapeutic product, we combined a detailed comparative static analysis and dynamic analysis along with conformational free energy and secondary structure prediction. We observed that the high intramolecular interactions and the geometrical features favored gramicidin-A among other types of gramicidin. Our analyses further revealed that the secondary structure of gramicidin-A showed ß sheets with coils along the conformations without any disruption, thereby enhanced its membrane interactions in terms of binding free energy. In conclusion, gramicidin-A has definitely showed enhanced structural stability and functionality; this could be considered the best template for a potential therapeutic product.

The structural and functional reliability of Circulins of Chassalia parvifolia for peptide therapeutic scaffolding.

Computational methods have refined the mode of peptide drug designing to a new plateau recently. Circulin, a 30 residue natural plant polypeptide acts as a plant defensive peptide. Additional to its antimicrobial activity it also possesses an inhibitory cytopathic effect on the replication of human immunodeficiency virus (HIV). Stable Circulin can be a functionally able template for scaffolding peptide based drugs. Hence, structural stability of Chassalia parvifolia, Circulin A (1BH4), and Circulin B (2ERI) was computationally investigated. From this analysis, the stability favored toward Circulin B which was supported by various parameters such as intra-molecular interactions (61), secondary structure, hydrophobicity (67.34%), root mean square deviation (2.64Å), root mean square fluctuation (0.08Å), radius of gyration (8.96Å), ovality (3.49), angular deviation (73.6%), surface area (both polar and non-polar), hydrogen bond distribution (11.94), and disulphide bond distances. Further, the functional activity calculated in terms of membrane associated free energy (-4.10 kcal/mol) also favored Circulin B. Hence, Circulin B could be proposed as the best template for scaffolding antimicrobial as well as antiviral (HIV) peptide based drug design. The obtained computational data can aid experimental biologists to successfully produce stable therapeutic peptides from natural resources reducing erroneous wastage of monetary sources and time.

Deciphering the Molecular Effects of Mutations on ATRX Cause ATRX Syndrome: A Molecular Dynamics Study.

α-thalassemia mental retardation X-linked (ATRX) syndrome is caused by the dysfunction of ATRFfigX protein. The present study explored the structural consequences influenced by two observed mutations V194I and C220R on ADD domain of ATRX protein by applying all atom molecular dynamics (MD) simulation. MD result showed that both the mutants exhibited wide variations in their backbone dynamics, as a result, mutant V210I showed complete distortion on α3 and the mutant C220R displayed a biased disruption on α2-3. The interference in the local folding of α-helices in both the mutants resulted by the loss of hydrogen bonds mediated by the backbone atoms. Principle component analysis (PCA) elucidated that both the mutants endured a diverse conformational dynamics, consequently adopted thermodynamically different conformational state. Besides, binding residues in both the mutants showed more structural disorder, thereby unable to recognize the hallmark modification, K9me3 (tri-methylated lysine at position 9) of histone H3 peptide and it was not conducive for the wild type ADD domain like functionality. Altogether, our findings provide knowledge to understand the structural and functional relationship of disease-associated mutations, V194I and C220R on ADD domain as well as gain further insights into the molecular pathogenesis of ATRX syndrome. J. Cell. Biochem. 118: 3318-3327, 2017. © 2017 Wiley Periodicals, Inc.

Unraveling the molecular effects of mutation L270P on Wiskkot-Aldrich syndrome protein: insights from molecular dynamics approach.

Missense mutation L270P disrupts the auto-inhibited state of "Wiskkot-Aldrich syndrome protein" (WASP), thereby constitutively activating the mutant structure, a key event for pathogenesis of X-linked neutropenia (XLN). In this study, we comprehensively deciphered the molecular feature of activated mutant structure by all atom molecular dynamics (MD) approach. MD analysis revealed that mutant structure exposed a wide variation in the spatial environment of atoms, resulting in enhanced residue flexibility. The increased flexibility of residues favored to decrease the number of intra-molecular hydrogen bonding interactions in mutant structure. The reduction of hydrogen bonds in the mutant structure resulted to disrupt the local folding of secondary structural elements that eventually affect the proper folding of mutants. The unfolded state of mutant structure established more number of inter-molecular hydrogen bonding interaction at interface level due to the conformational variability, thus mediated high binding affinity with its interacting partner, Cdc42.