Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Unveiling the binding interaction of zinc (II) complexes of homologous Schiff-base ligands on the surface of BSA protein: A combined experimental and theoretical approach

Four new zinc (II) complexes [Zn (HL¹H)Br₂] (1), [Zn (HL¹H)Cl₂] (2), [Zn₂(HL²)Br₃] (3), and [Zn (HL²)Cl] (4) have been synthesized by adopting template synthetic strategy and utilizing two homologous Schiff base ligands (H₂L¹ = 4-bromo-2-{[2-(2-hydroxyethylamino)-ethylimino]-methyl}-6-methoxyphenol, H₂L² = 4-bromo-2-{[3-(2-hydroxyethylamino)propylimino]methyl}-6-methoxyphenol), differing in one -CH₂- unit in the ligating backbone, by adopting template synthetic strategy. All the complexes have been characterized by single crystal X-ray diffraction analysis as well as by other routine physicochemical techniques. Ligand mediated structural variations have been observed and rationalized by density functional theoretical (DFT) calculations. Interaction of the complexes 1–4 with Bovine Serum Albumin protein (BSA) has been studied by different spectroscopic techniques. A complete thermodynamic profile (ΔH^o, ΔS^o and ΔG^o) was evaluated initially from the change in absorption and fluorescence spectra upon addition of BSA to the complexes. Appreciable binding constant values in the range ~ 0.94–4.51 × 10⁴ M⁻¹ indicate efficient binding tendency of the complexes to BSA with the sequence 1 ≅ 2 > 3 ≅ 4. Circular dichroism (CD), isothermal calorimetric titration experiments, molecular docking and molecular dynamics have been performed to gain deep insight into the binding regions of complex 1 to BSA. Experimental evidences suggest an interaction of zinc complexes at the surface of BSA protein and this particular binding has been exploited to determine unknown concentration of BSA protein. For this purpose complex 1 was explored as a BSA protein quantification tool.     

Thermal decomposition of model compound of algal biomass

This contribution investigates thermal decomposition of leucine, as a representative model compound for amino acids in algal biomass. We map out potential energy surface for a wide array of unimolecular and self-condensation reactions operating in the decomposition of leucine. Decarboxylation and dehydration of leucine ensues by eliminating CO₂ and –OH, respectively, from the –COOH group attached to the α-carbon. The molecular channel for deamination involves cleavage of NH₂ from α-carbon of leucine. The activation energies for direct elimination of CO₂, NH₃, and H₂O from a leucine molecule lie within 20.7 kJ/mol of each other. Activation energies for these decomposition pathways reside below the bond dissociation enthalpy of H–C(α) of 323.1 kJ/mol. The decarboxylation, deamination, and dehydration pathways, via radical-prompted pathways, systematically require lower energy barriers, in reference to closed-shell reaction corridors. Detailed computations at the CBS-QB3 level provide the Arrhenius rate parameters for the unimolecular and bimolecular reactions, and standard enthalpies of formation, standard entropies, and heat capacities for all the products and intermediates. A kinetic analysis of gas-phase reactions, within the context of a plug-flow reactor model, accounts qualitatively for the formation of major products observed experimentally in the thermal degradation of the condensed-phase leucine. Among notable N-containing species, the model predicts the prevailing of NH₃ over HCN and HNCO, in addition to corresponding appreciable concentrations of amines, imines, and nitriles. Our detailed kinetic investigation illustrates a negligible contribution of the self-condensation reactions of leucine in the gas phase.     

Different PES nanofibrous membrane parameters effect on the efficacy of immunoassay performance

The contribution of electrospun nanofibrous membranes (e.NFMs) in the biosensing platforms opens up a new prospect for the invention of faster and more sensitive analytical devices. In this paper, we utilized e.NFM of polyethersulfone (PES) as a solid substrate for the protein immobilization through two different approaches: physical and covalent. Scanning electron microscopy (SEM) and Fourier‐transform‐infrared (FTIR) tests were performed to study the effect of plasma treatment on protein immobilization efficacy. Moreover, taking advantage of ELISA technique, the influence of different parameters, namely, nanofibers diameter, membrane thickness, plasma treatment time, an incubation time of ethyl‐3‐(3‐dimethylaminopropyl)‐carbodiimide/N‐hydroxysuccinimide (EDC/NHS), and their ratio on antibody immobilization efficacy through two mentioned approaches, was also assessed.     

Biological and catalytic evaluation of Ru(II)‐p‐cymene complexes of Schiff base ligands: Impact of ligand appended moiety on photo‐induced DNA and protein cleavage,cytotoxicity and C‐H activation

Two organometallic Ru(II)‐p‐cymene complexes of the type [Ru(η⁶‐p‐cymene)(L)Cl]PF₆ 1 and 2 , where L is N,N‐bis(4‐isopropylbenzylidene)ethane‐1,2‐diamine (bien, L1 ) or N,N‐bis (pyren‐2‐ylmethylene)ethane‐1,2‐diamine (bpen, L2 ) have been prepared and characterized well. Because of appended pyrenyl groups in coordinated bpen ligand, the complex 2 exhibits higher DNA and protein binding than complex 1 in which isopropylbenzyl groups are incorporated. Interestingly, the luminescent characteristic complex 2 is unique in displaying DNA cleavage after light activation by UVA light at 365 nm through oxygen dependent mechanism. AFM analysis attests the photo‐induced DNA fragmentation ability of complex 2 . Also, the complex 2 cleaves the protein after light exposure in a non‐specific manner suggesting that it can act as a protein photo cleaving agent. In contrast to the trend of DNA and protein interaction of complexes, the complex 1 exhibits cytotoxic activity against human breast carcinoma ( MCF‐7 ) and liver carcinoma ( HepG2 ) with potency higher than that of complex 2 due to enhanced hydrophobicity of isopropyl groups present in p‐cymene and bien ligands. Indeed, complex 2 is inactive against MCF‐7 and HepG2 cancer cell lines even up to 200 μM concentration. The AO/EB staining assay reveals that the complex 1 is able to induce late apoptotic mode of cell death in breast cancer cells, which is further confirmed by inter‐nucleosomal DNA cleavage. Furthermore, the complexes 1 and 2 are evaluated for their catalytic activities and found to be working well for the β‐carboline directed C–H arylation to afford the desired products in good yield (40–47%).     

Single-Step N-Terminal Modification of Proteins via a Bio-Inspired Copper(II)-Mediated Aldol Reaction

The chemical modification of proteins is an effective technique for manipulating the properties and functions of proteins, and for creating protein-based materials. The N-terminus is a promising target for single-site modification that provides modified proteins with uniform structures and properties. In this paper, a copper(II)-mediated aldol reaction with 2-pyridinecarboxaldehyde (2-PC) derivatives is proposed as an operationally simple method to selectively modify the N-terminus of peptides and proteins at room temperature and physiological pH. The copper(II) ion activates the N-terminal amino acids by complexation with an imine of the N-terminal amino acid and 2-PCs, realizing the selective formation of the nucleophilic intermediate at the N-terminus. This results in a stable carbon-carbon bond between the 2-PCs and the α-carbon of various N-terminal amino acids. The reaction is applied to four different proteins, including biopharmaceuticals such as filgrastim and trastuzumab. The modified trastuzumab retains the human epidermal growth factor receptor 2 recognition activity.     

Comparative structural analysis of a histone-like protein from Spiroplasma melliferum in the crystalline state and in solution

A solution of a histone-like protein from Spiroplasma melliferum (HUSpm) was examined by small-angle X-ray scattering (SAXS). The experimental SAXS curve was compared with those calculated for the HUSpm structures from the PDB databank obtained by both X-ray diffraction analysis and nuclear magnetic resonance spectroscopy. The model of the HUSpm structure in solution, which best agrees with the experimental SAXS data, has a shorter distance between the centers of mass of the HUSpm monomers compared to the crystal structure, indicating that the HUSpm monomers can be located closer to each other in solution than in the crystalline state.     

Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.     

Atomistic insights into the selective therapeutic activity of 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a]pyrazin-1(2H)-one towards bromodomain-containing proteins

Cross-target effect has been one of the major mechanisms of drug toxicity, this has necessitated the design of inhibitors that are specifically tailored to target particular biomolecules. 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a] pyrazin-1(2H)-one (Cpd38) is an inhibitor possessing high inhibition rate and tailored specificity towards bromodomain-containing protein 4 (BRD4). In this research, we used an array of computational techniques to provide insight at the atomistic level the specific targeting of BRD4 by Cpd38 relative to the binding of Cpd38 with E1A binding protein P300 (EP300); another bromodomain-containing protein (BCP). Comparatively, binding of Cpd38 improved the conformational stability and compactness of BRD4 protein when compared to the Cpd38 bound EP300. Also, Cpd38 induced a conformational change in the active site of BRD4 that facilitated a complementary pose between Cpd38 and BRD4 suitable for effective atomistic interactions. Expectedly, thermodynamic calculations revealed that the Cpd38-BRD4 system had higher binding energy (−36.11 Kcal/mol) than the Cpd38-EP300 system with a free binding energy of −15.86 Kcal/mol. Noteworthy is the opposing role Trp81 (acting as hydrogen bond acceptor) and Pro1074 (acting as hydrogen bond donor) found on the WPF and LPF loops respectively play in maintaining Cpd38 stability. Furthermore, the hydrogen bond acceptor/donator ratio was approximately 4:1 in Cpd38-BRD4 system compared with 2:1 in Cpd38-EP300 system. Taken together, atomistic insights and structural perspectives detailed in this report supplements the experimental report supporting the improved selectivity of Cpd38 for BRD4 ahead of other BCPs while providing leeway for the future design of BET selective agents with better pharmacological profile.     

Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors

Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.