Atomic Contacts Research Articles

Identification of Homeobox Transcription Factors in a Dimorphic Fungus Talaromyces marneffei and Protein-Protein Interaction Prediction of RfeB.

Talaromyces marneffei is a thermally dimorphic fungus that can cause life-threatening systemic mycoses, particularly in immunocompromised individuals. Fungal homeobox transcription factors control various developmental processes, including the regulation of sexual reproduction, morphology, metabolism, and virulence. However, the function of homeobox proteins in T. marneffei has not been fully explored. Here, we searched the T. marneffei genome for the total homeobox transcription factors and predicted their biological relevance by performing gene expression analysis in different cell types, including conidia, mycelia, yeasts, and during phase transition. RfeB is selected for further computational analysis since (i) its transcripts were differentially expressed in different phases of T. marneffei, and (ii) this protein contains the highly conserved protein-protein interaction region (IR), which could be important for pathobiology and have therapeutic application. To assess the structure-function of the IR region, in silico alanine substitutions were performed at three-conserved IR residues (Asp276, Glu279, and Gln282) of RfeB, generating a triple RfeB mutated protein. Using 3D modeling and molecular dynamics simulations, we compared the protein complex formation of wild-type and mutated RfeB proteins with the putative partner candidate TmSwi5. Our results demonstrated that the mutated RfeB protein exhibited increased free binding energy, elevated protein compactness, and a reduced number of atomic contacts, suggesting disrupted protein stability and interaction. Notably, our model revealed that the IR residues primarily stabilized the RfeB binding sites located in the central region (CR). This computational approach for protein mutagenesis could provide a foundation for future experimental studies on the functional characterization of RfeB and other homeodomain-containing proteins in T. marneffei.

Recursive dynamics of GspE through machine learning enabled identification of inhibitors

Type II secretion System has been increasingly recognized as a key driver of virulence in many pathogenic bacteria including Achromobacter xylosoxidans. ATPase GspE is the powerhouse of the T2SS. It powers the entire secretion process by binding with ATP and hydrolyzing it. Therefore, targeting it was thought to have a profound effect on the normal functioning of the whole T2SS. A. xylosoxidans is a Gram-negative bacterium that poses a rising concern to immunocompromised people. It is responsible for many opportunistic infections mostly in people with cystic fibrosis. Due to its intrinsic and acquired resistance mechanisms, it is challenging to treat. In this current study, an extensive machine learning-enabled computational investigation was carried out. Drug libraries were screened using machine learning random forest algorithm trained on non-redundant dataset of 8722 antibacterial compounds with reported IC50 values. Active compounds were then further subjected to molecular docking. To unravel the dynamics and better understand the stability of complexes, the top complexes were subjected to MD Simulations followed by various post-simulation analyses including Trajectory analysis, Atom Contacts, SASA, Hydrogen Bond, RDF, binding free energy calculations, PCA, and AFD analysis. Findings from the study unanimously unveiled Asinex-BAS00263070–28551 as the best inhibitor as it instigated the recursive dynamics of the target by making key hydrogen bond interactions with Walker A motif, suggesting it could serve as the promising drug candidate against GspE. Further experimental in-vivo and in-vitro validation is still required to authenticate the therapeutic effects of these drugs.

Mechanical force regulates ligand binding and function of PD-1.

Despite the success of PD-1 blockade in cancer therapy, how PD-1 initiates signaling remains unclear. Soluble PD-L1 is found in patient sera and can bind PD-1 but fails to suppress T cell function. Here, we show that PD-1 function is reduced when mechanical support on ligand is removed. Mechanistically, cells exert forces to PD-1 and prolong bond lifetime at forces <7 pN (catch bond) while accelerate dissociation at forces >8pN (slip bond). Molecular dynamics of PD-1-PD-L2 complex suggests force may cause relative rotation and translation between the two molecules yielding distinct atomic contacts not observed in the crystal structure. Compared to wild-type, PD-1 mutants targeting the force-induced distinct interactions maintain the same binding affinity but suppressed/eliminated catch bond, lowered rupture force, and reduced inhibitory function. Our results uncover a mechanism for cells to probe the mechanical support of PD-1-PD-Ligand bonds using endogenous forces to regulate PD-1 signaling.

New polymorph of N-benzoyl-morpholine-4-carbothioamide with ten crystallographically independent molecules in the asymmetric unit: Crystal structure, Hirshfeld surface analysis and Density functional theory calculations

Herein, facile synthesis, single crystal X-ray diffraction (SC-XRD) structure, Hirshfeld surface (HS) analysis and Density functional theory (DFT) calculations of N-benzoyl-morpholine-4-carbothioamide 5(a) are presented. Hence, the synthesized compound, C12H14N2O2S 5(a), crystallizes in monoclinic crystal system having space group of P 21 with a = 22.2226 (9) Å, b = 11.7520 (3) Å, c = 24.9361 (8) Å, α = 90°, β = 111.054 (4)°, γ = 90°, Z = 20 and V = 6077.6 (4) Å3. The asymmetric unit of 5(a) contains ten crystallographically independent molecules, where the morpholine and benzene rings are in respective chair and planar conformations. In the crystal structure, some of the intermolecular, N—H···O, C—H···O and C—H···S, hydrogen bonds link the molecules into a 2D-network parallel to (010), enclosing R22(10) and R22(24) ring motifs, when viewed down the b-axis direction. Furthermore, contribution of the remaining hydrogen bonds consolidates a 3D-architecture. Similarly, HS analysis clarified the importance of hydrogen atom contacts with the major contributions of H…H (46.7 %), H…S/S…H (21.1 %), H…C/C…H (16.5 %), and H…O/O…H (12.5 %). Thus, hydrogen bond and van der Waals interactions play major role in the crystal packing. Finally, optimum molecular structure of compound 5(a) was related to the experimentally determined one employing DFT at B3LYP/6–311++G(d,p) level. Subsequently, the geometry of the optimized and most stable conformation turned out to be complementary with the crystal structure. The computational calculation of compound 5(a) revealed the molecule to be chemically hard in nature with high energy intrinsic reaction pathway. The associated band gap predicted compound 5(a) to be a wide band gap material. The intrinsic reaction pathway predicts hard-core behavior of the molecule.

In vitro and in silico studies of the inclusion complexation of 8-bromobaicalein with β-cyclodextrins

Baicalein, a flavone derived from Scutellaria baicalensis Georgi, exhibits potent anti-inflammatory, antiviral, and anticancer properties. Its derivative, known as 8-bromobaicalein (BB), has been found to have strong cytotoxic effect on MCF-7 human breast cancer cells. However, its limited solubility in water has hindered its potential for wider applications. To address this issue, we investigated the use of cyclodextrins specifically βCD, 2,6-di-O-methyl-β-cyclodextrin (DMβCD), and hydroxypropyl-β-cyclodextrin (HPβCD) to improve the solubility of BB through inclusion complexation. During 250 ns molecular dynamics simulations, it was found that BB can form inclusion complexes with all βCDs. These complexes exhibit two distinct orientations: chromone group insertion (C-form) and phenyl group insertion (P-form). The formation of these complexes is primarily driven by van der Waals interactions. DMβCD has the highest number of atom contacts with BB and the lowest solvent accessibility in the hydrophobic cavity. These results coincide with the highest binding affinity from the MM/GBSA-based free energy calculation method. Experimental phase solubility diagrams revealed a 1:1 stoichiometric ratio (AL type) between BB and βCDs, in which BB/DMβCD showed the highest stability. The formation of inclusion complexes was confirmed by differential scanning calorimetry and scanning electron microscope methods. Additionally, the BB/DMβCD inclusion complex demonstrated significantly higher anticancer activity against MCF-7 human breast cancer cells compared to BB alone. These findings underscore the potential of DMβCD for formulating BB in pharmaceutical and medical applications.

Crystal structure and Hirshfeld surface analysis of 2-bromo-ethyl-ammonium bromide - a possible side product upon synthesis of hybrid perovskites.

This study presents the synthesis, characterization and Hirshfeld surface analysis of a small organic ammonium salt, C2H7BrN+·Br-. Small cations like the one in the title compound are considered promising components of hybrid perovskites, crucial for optoelectronic and photovoltaic applications. While the incorporation of this organic cation into various hybrid perovskite structures has been explored, its halide salt counterpart remains largely uninvestigated. The obtained structural results are valuable for the synthesis and phase analysis of hybrid perovskites. The title compound crystallizes in the solvent-free form in the centrosymmetric monoclinic space group P21/c, featuring one organic cation and one bromide anion in its asymmetric unit, with a torsion angle of -64.8 (2)° between the ammonium group and the bromine substituent, positioned in a gauche conformation. The crystal packing is predominantly governed by Br⋯H inter-actions, which constitute 62.6% of the overall close atom contacts.

Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation

Oxyresveratrol (OXY), a natural stilbenoid in mulberry fruits, is known for its diverse pharmacological properties. However, its clinical use is hindered by low water solubility and limited bioavailability. In the present study, the inclusion complexes of OXY with β-cyclodextrin (βCD) and its three analogs, dimethyl-β-cyclodextrin (DMβCD), hydroxypropyl-β-cyclodextrin (HPβCD) and sulfobutylether-β-cyclodextrin (SBEβCD), were investigated using in silico and in vitro studies. Molecular docking revealed two binding orientations of OXY, namely, 4′,6′-dihydroxyphenyl (A-form) and 5,7-benzenediol ring (B-form). Molecular Dynamics simulations suggested the formation of inclusion complexes with βCDs through two distinct orientations, with OXY/SBEβCD exhibiting maximum atom contacts and the lowest solvent-exposed area in the hydrophobic cavity. These results corresponded well with the highest binding affinity observed in OXY/SBEβCD when assessed using the MM/GBSA method. Beyond traditional simulation methods, Ligand-binding Parallel Cascade Selection Molecular Dynamics method was employed to investigate how the drug enters and accommodates within the hydrophobic cavity. The in silico results aligned with stability constants: SBEβCD (2060 M−1), HPβCD (1860 M−1), DMβCD (1700 M−1), and βCD (1420 M−1). All complexes exhibited a 1:1 binding mode (AL type), with SBEβCD enhancing OXY solubility (25-fold). SEM micrographs, DSC thermograms, FT-IR and 1H NMR spectra confirm the inclusion complex formation, revealing novel surface morphologies, distinctive thermal behaviors, and new peaks. Notably, the inhibitory impact on the proliferation of breast cancer cell lines, MCF-7, exhibited by inclusion complexes particularly OXY/DMβCD, OXY/HPβCD, and OXY/SBEβCD were markedly superior compared to that of OXY alone.

A comprehensive study on the intermolecular interactions and energy frameworks exist in crystal structures of Form-I, Form-II and Form-III polymorphs of Ethyl maltol

The present study serves as a comprehensive investigation into the molecular crystal structures of three polymorphic forms of ethyl maltol. Crystal structures of the polymorphs grown via slow evaporation and quench cooling crystallization processes were determined through single crystal X-ray diffraction (SCXRD) analysis. Through the utilization of SCXRD data CIF file as an input, we explored the nature and strength of intermolecular interactions, atom pair close contacts, interaction types, 2D fingerprint plots, surface characteristics and percentage of voids present within each polymorph of ethyl maltol. The comparative analysis involves the application of advanced methods, such as Hirshfeld surface analysis and 3D-energy frameworks using Crystal Explorer 17.5. In a supramolecular organization, intermolecular interaction between the carbonyl and hydroxyl groups is a collective structural motif employed among the three polymorphs. However the three polymorphs share common structural features, but the conformations within the crystal packing of each form are different from each other. Shape Index and Curvedness surfaces reveal π stacking interactions with varying properties on differing sides of the molecular moieties between the polymorph. Fingerprint analysis emphasizes that (H…H) is the predominant interaction whereas (O…H) and (H…O) interactions contribute more towards the generation of H-bond interactions in the structure of ethyl maltol polymorphs. The crystal structures of all the three ethyl maltol polymorphs stabilized by various intermolecular contacts within the Hirshfeld surface area was comparable. The interaction energy and the 3D-energy frameworks offer a visualization of the crystal packing topology, enhancing our understanding of the three-dimensional arrangement of molecules and their structural stability. The resulting overall average total energy values for Form-I, Form-II and Form-III polymorphs of ethyl maltol are -56.3 kJ /mol, -74 kJ /mol and -80.45 kJ /mol respectively which reveals that all the three polymorphs show a significant difference in their total energies and reveals further that Form-III polymorph of ethyl maltol is the most stable one while Form-I is the least stable and Form-II is metastable relatively. Moreover, the dispersion energy framework is predominant over the electrostatic energy framework. The void analysis reveals the percentage of volume occupied by the voids present in the unit cell of Form-I, Form-II, and Form-III polymorphs of ethyl maltol are found to be 7.20%, 6.55 %, and 9.43% respectively.

Chromophore-Protein Interactions Affecting the Polyene Twist and π-π* Energy Gap of the Retinal Chromophore in Schizorhodopsins.

The properties of a prosthetic group are broadened by interactions with its neighboring residues in proteins. The retinal chromophore in rhodopsins absorbs light, undergoes structural changes, and drives functionally important structural changes in proteins during the photocycle. It is therefore crucial to understand how chromophore-protein interactions regulate the molecular structure and electronic state of chromophores in rhodopsins. Schizorhodopsin is a newly discovered subfamily of rhodopsins found in the genomes of Asgard archaea, which are extant prokaryotes closest to the last common ancestor of eukaryotes and of other microbial species. Here, we report the effects of a hydrogen bond between a retinal Schiff base and its counterion on the twist of the polyene chain and the color of the retinal chromophore. Correlations between spectral features revealed the unexpected fact that the twist of the polyene chain is reduced as the hydrogen bond becomes stronger, suggesting that the twist is caused by tight atomic contacts between the chromophore and nearby residues. In addition, the strength of the hydrogen bond is the primary factor affecting the color-tuning of the retinal chromophore in schizorhodopsins. The findings of this study are valuable for manipulating the molecular structure and electronic state of the chromophore by controlling chromophore-protein interactions.

Enhancing solubility and stability of piperine using β-cyclodextrin derivatives: computational and experimental investigations

Piperine (PP), a natural alkaloid found in black pepper, possesses significant bioactivities. However, its use in pharmaceutical applications is hindered by low water solubility and susceptibility to UV light degradation. To overcome these challenges, we investigated the potential of β-cyclodextrin (βCD) and its derivatives with dimethyl (DMβCD), hydroxy-propyl (HPβCD) and sulfobutyl-ether (SBEβCD) substitutions to enhance the solubility and stability of PP. This study employed computational and experimental approaches to examine the complexation between PP and βCDs. The results revealed the formation of two types of inclusion complexes: the P-form and M-form involving the insertion of piperidine moiety and the methylene-di-oxy-phenyl moiety, respectively. These complexes primarily rely on van der Waals interactions. Among the three derivatives, the PP/SBEβCD complex exhibited the highest stability followed by HPβCD, as attributed to maximum atom contacts and minimal solvent accessibility. Solubility studies confirmed the formation of inclusion complexes in a 1:1 ratio. Notably, the stability constant of the inclusion complex was approximately two-fold higher with SBEβCD and HPβCD compared to βCD. The DSC thermograms provided confirmation of the formation of the inclusion complex between the host and guest. These findings highlight the potential of βCD derivatives to effectively encapsulate PP, improving its solubility and presenting new opportunities for its pharmaceutical applications. Communicated by Ramaswamy H. Sarma

PRA-Pred: Structure-based prediction of protein-RNA binding affinity

Understanding crucial factors that affect the binding affinity of protein-RNA complexes is vital for comprehending their recognition mechanisms. This study involved compiling experimentally measured binding affinity (ΔG) values of 217 protein-RNA complexes and extracting numerous structure-based features, considering RNA, protein, and interactions between protein and RNA. Our findings indicate the significance of RNA base-step parameters, interaction energies, number of atomic contacts in the complex, hydrogen bonds, and contact potentials in understanding the binding affinity. Further, we observed that these factors are influenced by the type of RNA strand and the function of the protein in a protein-RNA complex. Multiple regression equations were developed for different classes of complexes to perform the prediction of the binding affinity between the protein and RNA. We evaluated the models using the jack-knife test and achieved an overall correlation 0.77 between the experimental and predicted binding affinities with a mean absolute error of 1.02 kcal/mol. Furthermore, we introduced a web server, PRA-Pred, intended for the prediction of protein-RNA binding affinity, and it is freely accessible through https://web.iitm.ac.in/bioinfo2/prapred/. We propose that our approach could function as a potential resource for investigating protein-RNA recognitions and developing therapeutic strategies.

Analysis of short contacts in crystals of halogenated amino acids: atom–atom interactions vs. energy frameworks

Crystal packing of several halogenated alanine derivatives was investigated using the combined analysis of short atom–atom contacts and energy framework patterns.

GraSp-PSN: A web server for graph spectra based analysis of protein structure networks

The function of a protein is most of the time achieved due to minute conformational changes in its structure due to ligand binding or environmental changes or other interactions. Hence the analysis of structure of proteins should go beyond the analysis of mere atom contacts and should include the emergent global structure as a whole. This can be achieved by graph spectra based analysis of protein structure networks. GraSp-PSN is a web server that can assist in (1) acquiring weighted protein structure network (PSN) and network parameters ranging from atomic level to global connectivity from the three dimensional coordinates of a protein, (2) generating scores for comparison of a pair of protein structures with detailed information of local to global connectivity, and (3) assigning perturbation scores to the residues and their interactions, that can prioritise them in terms of residue clusters. The methods implemented in the server are generic in nature and can be used for comparing networks in any discipline by uploading adjacency matrices in the server. The webserver can be accessed using the following link: https://pople.mbu.iisc.ac.in/.

Computational study of conductance through Cu, Ag, Au and Pt atomic chain contacts

Atomic size wires are basic devices of molecular electronics and a common model for simulation of transport properties of other molecular devices, where hypothetical semi-infinite equidistant atomic chains are considered as electrodes. In this work, structure of infinite linear Cu, Ag, Au and Pt atomic chains was studied at nonrelativistic, scalar and spin–orbit zeroth order relativistic approximation levels. Bonds in chains were characterized within Quantum Theory of “Atoms In Molecules” approach. Conductance through finite chains of six atom length between bulk leads for bias voltage range of 0.0–1.0 V was calculated within non-equilibrium Green’s function approach combined with density functional theory. Chain conductance at high bias voltages correlates with product of Jenkins’ metallicity and positively defined kinetic energy density at bond critical points of corresponding infinite atomic chains. Variation of number of atoms in finite Au and Pt chains showed weak “odd-even” oscillations of chain conductance at some bias voltages.

Bond Breaking Kinetics in Mechanically Controlled Break Junction Experiments: A Bayesian Approach.

Break junction experiments allow investigating electronic and spintronic properties at the atomic and molecular scale. These experiments generate by their very nature broad and asymmetric distributions of the observables of interest, and thus, a full statistical interpretation is warranted. We show here that understanding the complete lifetime distribution is essential for obtaining reliable estimates. We demonstrate this for Au atomic point contacts by adopting Bayesian reasoning to make maximal use of all measured data to reliably estimate the distance to the transition state, x‡, the associated free energy barrier, ΔG‡, and the curvature, v, of the free energy surface. Obtaining robust estimates requires less experimental effort than with previous methods and fewer assumptions and thus leads to a significant reassessment of the kinetic parameters in this paradigmatic atomic-scale structure. Our proposed Bayesian reasoning offers a powerful and general approach when interpreting inherently stochastic data that yield broad, asymmetric distributions for which analytical models of the distribution may be developed.

Structure elucidation, DFT and IRI computational investigations of a novel 4-(3-(4-chlorophenyl)-1-phenyl-1H-pyrazol-4-yl)2,6-dimethyl-1,4-dihydropyridine-3,5-dicarbonitrile

A novel symmetric dihydropyridine possessing cyano group at C11 and C14 has been synthesized using a modified Hantzsch method. The compound (▪) was characterized spectroscopically by Mass, IR and 1H NMR methods and finally confirmed by X-ray diffraction study. The compound crystallizes in a monoclinic crystal class with P21/c space group. In the title molecule, the dihydropyridine ring is puckered and displayed an envelope conformation of the type E1. The solid state of the title compound is governed by an intermolecular C–H…N, C–H…Cl and C–H…π interactions in the building of a crystal. It is investigated by three dimensional Hirshfeld surfaces mapped on different properties, also the relevant fingerprint graphs are obtained to recognize the percentage contribution from various inter atomic contacts. The topology of three dimensional interaction energy frameworks were constructed using the energy density wave function of DFT/B3LYP/6-311++G(d,p) and the energy corresponding to intermolecular interactions were assessed. The density functional theory analysis has been carried out and hence an energy gap and global index parameters are evaluated, also the geometric parameters are computed by optimizing the molecular structure of the title compound. The natural bonding orbitals (NBO) analysis is carried out to know the intermolecular charge transfer in the molecule. Reduced density gradients (RDG) and interaction region indicators (IRI) analysis reveals the chemical bonding and weak interactions regions. The molecular docking has been performed on 1B38, 2OHM, 3VNT and 4URO receptors shows good binding affinities and their results reveal that it serves as potential anti-cancer agent.

Layer Engineered MXene Empowered Wearable Pressure Sensors for Non‐Invasive Vital Human–Machine Interfacing Healthcare Monitoring

AbstractPressure sensors with high flexibility and sensitivity face significant challenges in meeting the delicate balance and synergy among suitable active sensing electrode materials, substrates, and their device geometry design. In this contribution, layer‐engineered delaminated Ti‐MXene (DL‐Ti3C2Tx) is introduced, which has relatively wider interlayer spacing through intercalated large organic molecules and accordion‐like open internal microstructure than the narrower pristine Ti3C2Tx MXene (Ti‐MXene), graphene/carbon nanotube's interlayer spacing suitably fulfill the high sensitivity and flexibility requirement through accessible electronic pathways under the external pressure. Notably, a milder in‐situ ambient condition etching is performed to eliminate the associated safety risks for a flexible personal healthcare monitoring pressure sensor. DL‐Ti3C2Tx MXene‐empowered, flexible pressure sensor demonstrates a broad range of sensitivities up to a very high‐pressure of 20.8 kPa at a sensitivity of 242.3 kPa−1 with a fast response and recovery time (&lt;300 ms). A twofold increase in pressure sensitivity performance of DL‐Ti3C2Tx MXene than that of Ti‐MXene, graphene can be attributed to the engineered wider interlayer distance among the delaminated DL‐Ti3C2Tx MXene layers causing a facile interlayer atomic movements, contacts, and reversible compressibility. The current economical, scalable DL‐Ti3C2Tx MXene flexible pressure sensor can provide future safe personal healthcare artificial intelligence with real‐time tracking ability.

Synthesis and crystal structure of bis-(9-mesityl-9,10-di-hydro-10-aza-9-borabenzo[h]quinolinato-κ2N1,N10)zinc(II).

The title compound, [Zn(C20H18BN2)2] (Zn L 2), is an overall uncharged chelate that consists of two units of an NH-deprotonated 10-aza-9-borabenzo[h]quinoline ligand (L) per ZnII center. It was synthesized in two steps by treating the protonated ligand HL with lithium bis-(tri-methyl-sil-yl)amide and further conversion with di-ethyl-zinc. Its asymmetric unit comprises one ZnL fragment; the mol-ecule is completed by application of inversion symmetry at Zn. Due to the fourfold coordination with nitro-gen atoms, the zinc(II) ion is located in a distorted tetra-hedral environment. Besides the relatively short N-Zn bonds, Zn L 2 is characterized by the significant protrusion of the central ion from the plane of the ligand backbone. The crystal structure is consolidated by intra- and inter-molecular π-π stacking inter-actions, while the polarized B-N bond is barely involved in any close atom contacts.

In Silico and In Vitro Potential of FDA-Approved Drugs for Antimalarial Drug Repurposing against Plasmodium Serine Hydroxymethyltransferases.

Malaria has spread in many countries, with a 12% increase in deaths after the coronavirus disease 2019 pandemic. Malaria is one of the most concerning diseases in the Greater Mekong subregion, showing increased drug-resistant rates. Serine hydroxymethyltransferase (SHMT), a key enzyme in the deoxythymidylate synthesis pathway, has been identified as a promising antimalarial drug target due to its conserved folate binding pocket. This study used a molecular docking approach to screen 2509 US Food and Drug Administration (FDA)-approved drugs against seven Plasmodium SHMT structures. Eight compounds had significantly lower binding energies than the known SHMT inhibitors pyrazolopyran(+)-86, tetrahydrofolate, and antimalarial drugs, ranging from 4 to 10 kcal/mol. Inhibition assays testing the eight compounds against Plasmodium falciparum SHMT (PfSHMT) showed that amphotericin B was a competitive inhibitor of PfSHMT with a half-maximal inhibitory concentration (IC50) of 106 ± 1 μM. Therefore, a 500 ns molecular dynamics simulation of PfSHMT/PLS/amphotericin B was performed. The backbone root-mean-square deviation of the protein-ligand complex indicated the high complex stability during simulations, supported by its radius of gyration, hydrogen-bond interactions, and number of atom contacts. The appreciable binding affinity of amphotericin B for PfSHMT was indicated by their solvated interaction energy (-11.15 ± 0.09 kcal/mol) and supported by strong ligand-protein interactions (≥80% occurrences) with its essential residues (i.e., Y78, K151, N262, F266, and V365) predicted by pharmacophore modeling and per-residue decomposition free energy methods. Therefore, our findings identify a promising new PfSHMT inhibitor, albeit with less inhibitory activity, and suggest a core structure that differs from that of previous SHMT inhibitors, thus being a rational approach for novel antimalarial drug design.

Electrically Controlled Bimetallic Junctions for Atomic-Scale Electronics.

Forming atomic-scale contacts with attractive geometries and material compositions is a long-term goal of nanotechnology. Here, we show that a rich family of bimetallic atomic-contacts can be fabricated in break-junction setups. The structure and material composition of these contacts can be controlled by atomically precise electromigration, where the metal types of the electron-injecting and sink electrodes determine the type of atoms added to, or subtracted from, the contact structure. The formed bimetallic structures include, for example, platinum and aluminum electrodes bridged by an atomic chain composed of platinum and aluminum atoms as well as iron-nickel single-atom contacts that act as a spin-valve break junction without the need for sophisticated spin-valve geometries. The versatile nature of atomic contacts in bimetallic junctions and the ability to control their structure by electromigration can be used to expand the structural variety of atomic and molecular junctions and their span of properties.