Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.     

Photoacoustic spectra and modes of vibration of TNT and RDX at CO2 laser wavelengths

IR spectra in the 'Finger Print' spectral range has great importance in qualitative and quantitative analysis of explosives like trinitrotoluene (TNT) and cyclotrimethyltrinitramine (RDX). Highly resolved IR bands of these compounds have been recorded in the 9.6 and 10.6 microm regions of CO2 laser. TNT and RDX are large molecules each having 21 atoms and it is very difficult to assign the modes of vibrations by comparison with those in other molecules making the vibrational assignments of observed bands a difficult task. The ab initio quantum chemical calculation is used for determining the molecular geometries and modes of vibration of these molecules with a view to assign their normal modes in the high resolution vibrational photoacoustic spectra. These assignments are very reliable in view of the good agreement between the observed and calculated frequencies of deuterated TNT.     

Microwave Induced Bismuth Trichloride Catalysed Beckmann Rearrangement of Oximes

A new and efficient method for the rearrangement of oximes 1 has been achieved by a simple reaction of a ketoximes with bismuth trichloride under microwave irradiation in the solid state.     

Structure‐cytotoxicity relationship for apoptotic inducers organotin(IV) derivatives of mandelic acid and L‐proline and their mixed ligand complexes having enhanced cytotoxicity

Structure‐cytotoxicity relationship of di?/tri‐organotin(IV) derivatives of mandelic acid ( 1 – 4 ), L‐proline ( 5 – 7, 15, 16 ), and mixed ligand complexes of latter with 1,10‐phenanthroline ( 8 – 14 ) investigated on the basis of MTT assay against human cancer cell lines, viz. MCF‐7 (mammary cancer), HepG2 (liver cancer) and PC‐3 (prostate cancer) in vitro indicated that all complexes except methyl‐ and octyl‐ analogues displayed potential cytotoxicity. The most active one is dibutyltin(IV) mandelate ( 2 ) exhibiting IC₅₀ 2.03 ± 0.40, 0.98 ± 0.23 and 3.86 ± 1.68 μM against MCF‐7, HepG2 and PC‐3, respectively, which is ≈ 15 and 2.5 times against MCF‐7, 20 and 5 times against HepG2 and 5 and ≈ 3 times against PC‐3 more cytotoxic than cis‐platin and 5‐fluorouracil, respectively. Diorganotin(IV) derivatives of mandelic acid are more cytotoxic than triorganotin analogues. Organotin(IV) derivatives of L‐proline (except Bu₃Sn(Pro) 16 ) are less cytotoxic than those of mandelic acid but their cytotoxicity is enhanced by complexion with 1,10‐phenanthroline. This may be due to the structural planarity and extended π system of 1,10‐phenanthroline which facilitates their transportation across the cell membrane and enhances the possibility of DNA intercalation over the planar L‐proline ring, and eventually, their DNA binding affinity so as to interfere with the cellular functions of DNA leading to apoptosis. Various biophysical experiments such as DNA fragmentation, acridine orange and comet assays, and flow cytometry assay using annexin V–fluorescein isothiocyanate (FITC) and propidium iodide (PI) have been carried out in order to ascertain their mode of action. The observed results indicated that the major cause of cancer cell death is apoptosis, but a minor role played by necrosis cannot be excluded. It is concluded on the basis of the observed results that the nature and number of organic groups bonded to tin as well as the nature of counter anions play an important role in determining the cytotoxicity of organotin(IV) compounds.     

RNAi for Insect Control: Current Perspective and Future Challenges

The research on the RNA interference (RNAi) for the control of insect pests has made significant growth in recent years. The availability of the genomic sequences of insects has further widened the horizons for the testing of this technology to various insect groups. Different modes of application of double-stranded RNA (dsRNA) have been tested; however, the practicability of delivery of dsRNA in insects still remains the biggest challenge. Till date, the oral delivery of dsRNA in insects is one of the efficient approaches for the practical application of this technique. The uptake of dsRNA from the insect gut is mediated either by SID-1/SID-2 transmembrane proteins or by endocytosis; however, the systemic RNAi machinery still remains to be revealed in insect species. The RNAi-mediated gene knockdown has shown striking results in different insect groups, pointing it to be the upcoming technique for insect control. However, before the successful application of this technique for insect control, some potential issues need to be resolved. This review presents the account of prospects and challenges for the use of this technology for insect control.     

Direct synthesis of Poly(Ԑ-Caprolactone)-block-poly (glycidyl methacrylate) copolymer and its usage as a potential nano micelles carrier for hydrophobic drugs

Ring-opening (ROP) and enzymatic copolymerization (ECP) are among the most widely used approaches for synthesizing copolymers of polycaprolactone (PCL). It involves multiple-step reactions and the utilization of enzymes that make the process a lot more complicated, time consuming, and expensive. Atom transfer radical polymerization (ATRP) has been adopted to synthesize a novel amphiphilic copolymer in our study. The study presents a method to eliminate the ROP/ECP multiple steps in monomer polymerization thus making the process simpler and smoother. The synthesis of cationic polymer micelles copolymer of PCL-PGMA (polycaprolactone grafted poly glycidyl methacrylate) was carried out using direct functionalization of hydroxy group in crude PCL to achieve a higher degree of functionalization, i.e., 12.8% for macroinitiator. FTIR and ¹H-NMR confirmed the successful synthesis of the copolymer with better control over the molecular weight with a PDI (1.84). DSC and XRD results showed the reduction of crystallinity by 86.81%, making copolymer more compatible for drug delivery application. The synthesized copolymer was further converted to nano-micelles drug carrier having an average size of 96.08 ± 21.22 nm. The drug encapsulation efficiency achieved was 60.0 ± 1.7%, and nano-micelles rendered a slow and controlled release of naproxen with long-term storage stability.