Structural insights into the binding mechanism of Plasmodium falciparum exported Hsp40-Hsp70 chaperone pair

Expression of heat shock proteins in Plasmodium falciparum (Pf) increases during febrile episodes to play key roles in several necessary cellular processes. ‘PFA0660w-PfHsp70-x’, an exported chaperone pair is known to co-localize to specialized intracellular structures termed J-dots, and has been implicated in trafficking of the major virulence factor, PfEMP1 (Plasmodium falciparum erythrocyte membrane protein 1) across the host cell. This article highlights for the first time detailed structural analysis of PFA0660w-PfHsp70-x chaperone pair to better understand their binding mechanism. Here, we have modeled reliable molecular structures for the complete conserved region of PFA0660w and PfHsp70-x. These structures were evaluated by different structure verification tools followed by molecular dynamics (MD) simulations. The model of PFA0660w was subjected to docking with PfHsp70-x using Haddock to reveal a number of residues crucial for their bipartite interaction, and also performed MD simulations on the complex. The peptide binding clefts of PFA0660w and its other Plasmodium species homologs were found to be bigger than their counterparts in higher eukaryotes like yeast, humans and C. parvum. Based on our results, we propose a model for PFA0660w-PfHsp70-x interaction and a mechanism of substrate binding, and compare it with its dimeric human counterparts. Owing to these striking structural differences between the host and parasite chaperones, such information on the essential Hsp40 and its partner Hsp70 may form the basis for rational drug design against fatal malaria.     

Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors

Dihydropteroate synthase (DHPS) is an alluring target for designing novel drug candidates to prevent infections caused by pathogenic Escherichia coli strains. Diaryl Sulfone (SO) compounds are found to inhibit DHPS competitively with respect to the substrate pABA (p-aminobenzoate). The extra aromatic ring of diaryl sulfone compounds found to stabilize them in highly flexible pABA binding loops. In this present study, a statistically significant 3D-QSAR model was developed using a data set of diaryl sulfone compounds. The favourable and unfavourable contributions of substitutions in sulfone compounds were illustrated by contour plot obtained from the developed 3D-QSAR model. Molecular docking calculations were performed to investigate the putative binding mode of diaryl sulfone compounds at the catalytic pocket. DFT calculations were carried out using SCF approach, B3LYP- 6-31 G (d) basis set to compute the HOMO, LUMO energies and their respective location at pABA binding pocket. Further, the developed model was validated by FEP (Free Energy Perturbation) calculations. The calculated relative free energy of binding between the highly potent and less potent sulfone compound was found to be −3.78 kcal/ mol which is comparable to the experimental value of −5.85 kcal/mol. A 10 ns molecular dynamics simulation of inhibitor and DHPS confirmed its stability at pABA catalytic site. Outcomes of the present work provide deeper insight in designing novel drug candidates for pathogenic Escherichia coli strains.     

New insights into the visible-light-induced DNA cleavage activity of dipyridoquinoxaline complexes of bivalent 3d-metal ions

Dipyridoquinoxaline (dpq) complexes of bivalent 3d-metal ions, viz., [FeII(dpq)3](PF6)2 (1), [CoII(dpq)3](ClO4)2 (2), [NiII(dpq)3](ClO4)2 (3), [CuII(dpq)2(H2O)](ClO4)2 (4), [ZnII(dpq)3](ClO4)2 (5), and [ZnII(dpq)2(DMF)2](ClO4)2 (5a) (DMF = N,N-dimethylformamide), are prepared and their photoinduced DNA cleavage activity studied. Structural characterization for the complexes 1 and 5a is done by single-crystal X-ray crystallography. All the complexes show efficient binding propensity to calf thymus DNA with a binding constant (K) value of approximately 10(5) M(-1). Complexes 1, 2, and 4 show metal-based cyclic voltammetric responses at 1.2, 0.4, and 0.09 V (vs SCE) in DMF 0.1 M [Bun4N](ClO4) assignable to the respective FeIII/FeII, CoIII/CoII, and CuII/CuI couples. The NiII and ZnII complexes do not show any metal-based redox process. The dpq-based reductions are observed in the potential range of -1.0 to -1.7 V vs SCE. DNA melting and viscosity data indicate the groove-binding nature of the complexes. Control experiments using distamycin-A suggest a minor groove-binding propensity of the complexes. The complexes exhibit photoinduced cleavage of supercoiled pUC19 DNA in UV light of 365 nm. The diamagnetic d6-FeII and d10-ZnII complexes are cleavage-inactive on irradiation with visible light. The paramagnetic d7-CoII and d9-CuII complexes exhibit efficient DNA cleavage activity on photoirradiation at their respective d-d band. The paramagnetic d8-NiII complex displays only minor DNA cleavage activity on irradiation at its d-d band. The DNA cleavage reactions at visible light under aerobic conditions involve the formation of hydroxyl radical. The CoII complex shows photocleavage of DNA under an argon atmosphere. Theoretical calculations on the complexes suggest a photoredox pathway in preference to a type-2 process forming singlet oxygen for the visible-light-induced DNA cleavage activity of the 3d-metal complexes. The theoretical data also predict that the photoredox pathway is favorable for the 3d7-CoII and 3d9-CuII complexes to exhibit DNA cleavage activity, while the analogous 3d6-FeII and 3d8-NiII complexes are energetically unfavorable for the exhibition of such activity under visible light. The CoII and CuII complexes are better suited for designing and developing new metal-based PDT agents than their cleavage-inactive FeII, NiII, and ZnII analogues.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

金属离子对HIV-1整合酶与硫氮硫扎平抑制剂作用模式影响的分子模拟研究

HIV-1整合酶（IN）通过依赖金属离子的两步反应将病毒DNA整合入宿主细胞过程中。结合于HIV-1上的金属离子个数的变化直接影响整合酶与抑制剂之间的结合。本工作用同源模建方法搭建了每条单链核心区具有两个Mg2+ 的（2Mg-IN-Core）和具有一个Mg2+ 的HIV-1 IN二聚体核心区模型（1Mg-IN-Core）。分子对接分别得到它们与硫氮硫扎平类化合物能量较低的复合物结构,把对接结果进行了比较。研究发现：当整合酶中结合的Mg2+个数改变时,它与抑制剂的结合模式也会发生很大的变化;抑制剂能够特异的且稳定的与2Mg-IN-Core模型的活性位点结合;同时与ASP64和GLU152螯合的那个Mg2+离子对于硫氮硫扎平抑制剂与整合酶上的结合有很大的影响。2Mg-IN-Core模型与抑制剂的复合物平均结构进行了2000 ps的 分子动力学模拟,分析发现同时与ASP64及ASP116螯合的Mg2+与IN蛋白形成了四个稳定的螯合键;同时与ASP64及GLU152螯合的Mg2+可与IN结合、也可与抑制剂形成稳定的配位键,这个Mg2+对IN与硫氮硫扎平抑制剂之间的结合有较大影响。     

Rational in silico design of aptamers for organophosphates based on the example of paraoxon

Poisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its three-dimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed.     

Exploring the effect of aplidin on low molecular weight protein tyrosine phosphatase by molecular docking and molecular dynamic simulation study

The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PTP could be remission. However, the molecular mechanism of inhibition of the LMW-PTP by the aplidin had not been fully understood. In this study, various computational approaches, namely molecular docking, MDs and post-dynamic analyses were utilized to explore the effect of the aplidin on the LMW-PTP. The results suggested that the intramolecular interactions of the residues in the two sides of the active site (Ser43-Ala55 and Pro121-Asn134) and the P-loop region (Leu13-Ser19) in the LMW-PTP was disturbed owing to the aplidin, meanwhile, the π-π interaction between Tyr131 and Tyr132 might be broken. The Asn15 might be the key residue to break the residues interactions. In a word, this study may provide more information for understanding the effect of inhibition of the aplidin on the LMW-PTP.     

Design,DFT studies,antimicrobial and antioxidant potential of Binuclear N-heterocyclic Carbene (NHCs) complexes,Probing the aspect of DNA interaction through In-vitro and In-silico approach

N-heterocyclic carbene (NHC) adducts have shown remarkable biological potential for numerous medical applications. With an aim to improve biological potential of benzimidazolium salts, newer analogues of benzimidazole and their silver complexes were synthesized and characterized. Synthesized salts (L₁-L₂) and silver complexes (C₁-C₂) were confirmed through elemental analysis, UV–visible spectroscopy, FTIR, ¹H NMR & ¹³C NMR spectroscopy. The compounds C1 & C2 were found stable in solution form for studied time period when examined spectroscopically and showed optimum lipophilicity when measured for their partition coefficient through flask shake method. Synthesized compounds showed good antimicrobial potential against gram positive bacterial strain S. Aureus with IC₅₀ 2.02±0.12 and 2.11±0.13 µM respectively while 2.11±0.1 and 2.28±0.17 µM against gram negative bacterial strain E. Coli for C1 and C2 respectively. The interaction study of the related compounds with DNA was predicted by molecular docking study, which confirmed that the studied compound C1 (-8.04 kcal/mol) has a higher binding energy than compound C2 (-4.23 kcal/mol); Also, the compound C1 exhibits a better affinity against to DNA than Ethidium bromide (-7.68 kcal/mol) and cisplatin (-6.21 kcal/mol).The claim was practically assured through spectroscopic and viscometeric method which confirmed that compounds have good affinity for DNA with binding constant kb, 5.78×10⁴ M^-1 and 6.84×10⁴ M^-1 for C1 and C2 respectively.     

Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain

Gelsolin is an actin-severing protein whose action is promoted by Ca²⁺ ions and inhibited by binding to lipid phosphoinositides incorporated in the inner leaflet of the plasma membrane inner lipid bilayer. In this study, we carried out molecular dynamics (MD) simulations to investigate the influence of calcium cations on the conformation of gelsolin S2 domain. First, gelsolin S2 domain taken from the crystal structure of apo-gelsolin (PDB code: 1D0N) was subjected to three 1100 ps MD simulations in a periodic water box with the 5.0 force field at T=298 K. In the first simulation (S2_Ca²⁺) excess concentration of Ca²⁺ was applied, in the second one (S2_phys) the concentration of Ca²⁺ ions was physiological and in the third one (S2_w) no Ca²⁺ ions were added. The results of MD simulations showed high conformational flexibility of the N-terminal part of the S2 domain. S2_w deviated from the starting structure considerably more that S2_phys and S2_Ca²⁺ suggesting that Ca²⁺ ions stabilize the conformation of the S2 domain of gelsolin.     

钙离子对表面活性剂单层膜聚集结构的影响

采用分子动力学模拟研究了气液界面上钙离子对阴离子表面活性剂十二烷基苯磺酸钠单层膜聚集结构的影响.结果表明,单层膜结构与表面覆盖度及Ca2＋离子存在与否均有关系.Ca2＋离子能够压缩表面活性剂极性头使聚集结构排列更加紧密,均力势体现了Ca2＋离子与极性头之间的结合能力强弱,二者之间的相互作用与稳定的溶剂分离极小值有关,而Ca2＋离子需要克服一个溶剂能障才能与之发生相互作用,并引起极性头周围水分子结构的重排.模拟表明,分子动力学方法可以在分子水平上研究无机盐离子对表面活性剂单层膜水化结构的影响,解释无机盐离子在界面膜中的动力学行为.     

Recent advances on hydrogels based on chitosan and alginate for the adsorption of dyes and metal ions from water

In contemporary times, water resources have become increasingly scarce and suffer from anthropogenic pollution sources with an organic and inorganic origin that are products of industrial, agricultural, and everyday waste. Contamination with heavy metals and dyes in wastewater is considered a risk for water sources that can leak into underground and surface sources, leading to increased biological and chemical contamination. The pollutant removal process is performed by adsorption treatment methods, which is the most common method, and it is considered an effective method with a high and economical removal rate.In this review, we discuss the use of biobased hydrogel adsorbents in the removal of organic dyes and metal ions from water. The literature indicates that hydrogels exhibit rapid absorption kinetics and a dye removal absorption capacity that can reach more than 100 mg/g and sometimes more than 2000 mg/g, with a metal adsorption capacity ranging from 38 mg/g to more than 440 mg/g. These results are discussed and compared by taking into account hydrogel materials that contain biopolymers such as alginate, chitosan or both. In general, absorption depends mainly on biobased materials, which have a natural origin and can be utilized to synthesize hydrogels to remove pollutants, dyes and heavy metals. Chitosan and alginate are prominent materials for this use and they can be incorporated with other components to obtain hydrogels or nanocomposite materials with different efficacies to remove dyes and metal ions.     

血管紧张素转换酶与抑制肽结合模式的分子动力学研究

应用分子模拟方法研究了血管紧张素转换酶(Angiotensin-converting enzyme,ACE)C端结构域(C-domain)与两种抑制肽(RIGLF/AHEPVK)的结合机制,预测了两个体系的结合模式,提出在C-domain-RIGLF中His353,Asp377,Asp453,Phe457,His513,Tyr523和Phe527为RIGLF主要结合残基,而在C-domainAHEPVK中Gln281,His353,Ser355,Glu384,Lys511,His513和Tyr523等残基起关键作用.应用结合自由能计算比较了两个体系的结合能力,结果表明,RIGLF和AHEPVK均与C-domain活性位点残基存在较强作用,且AHEPVK对C-domain的结合能力较强,与实验结果一致.     

The application and comparison of several chemometric methods of excitation-emission matrix spectra in studying the interactions of metal complexes with DNA

The interactions of fs DNA and two metal complexes [Cu(phen)SO₄]·2H₂O and [Ni(phen)SO₄]·2H₂O were explored by several chemometric methods, including parallel factor (PARAFAC), singular value decomposition-least squares (SVD-LS), and singular value decomposition-nonnegative least squares (SVD-NNLS) of excitation-emission matrix spectra (EEMs). The applications of SVD-LS and SVD-NNLS in this domain have been discussed. Rayleigh scatter part is avoided by ordered zero and reconstructed by linear interpolation. The importance of avoiding Rayleigh scatter has also been discussed. All the three methods do well in qualitative analysis. SVD-LS does best in present small changes of ethidium bromide (EB). In order to get accurate results, PARAFAC and SVD-NNLS can be utilized together in quantitative analysis. All the three chemometric methods indicate that the DNA binding modes of [Cu(phen)SO₄]·2H₂O are hydrogen bond effect and intercalation, while intercalation is the only DNA binding mode for [Ni(phen)SO₄]·2H₂O. These results are verified by the electronic absorption and emission fluorescence spectra. Just like PARAFAC, both SVD-LS and SVD-NNLS are proven to be convenient and convincing in studying the interactions between nucleic acids and complexes.     

Conformational changes of DNA molecules in interactions with bioactive compounds. I. Influence of metal ions on the conformation of DNA molecules in solution

The influence of metal ions of different valence on the conformation of DNA molecule in solution has been studied. The influence of concentration and charge of counterions on the volume, persistent length and secondary structure of the macromolecules was analyzed. An assessment of the permeability of DNA coil for the solvent at different values of ionic strength of the solution was made. The state of the DNA molecule in solutions with high ionic strengths, when the presence of certain ions causes sharp changes in optical anisotropy of the macromolecule, is considered in detail.     

Evaluation of potential MHC-I allele-specific epitopes in Zika virus proteins and the effects of mutations on peptide-MHC-I interaction studied using in silico approaches

Zika virus (ZIKV) infection is a global health concern due to its association with microcephaly and neurological complications. The development of a T-cell vaccine is important to combat this disease. In this study, we propose ZIKV major histocompatibility complex I (MHC-I) epitopes based on in silico screening consensus followed by molecular docking, PRODIGY, and molecular dynamics (MD) simulation analyses. The effects of the reported mutations on peptide-MHC-I (pMHC-I) complexes were also evaluated. In general, our data indicate an allele-specific peptide-binding human leukocyte antigen (HLA) and potential epitopes. For HLA-B44, we showed that the absence of acidic residue Glu at P2, due to the loss of the electrostatic interaction with Lys45, has a negative impact on the pMHC-I complex stability and explains the low free energy estimated for the immunodominant peptide E-4 (IGVSNRDFV). Our MD data also suggest the deleterious effects of acidic residue Asp at P1 on the pMHC-I stability of HLA-B8 due to destabilization of the α-helix and β-strand. Free energy estimation further indicated that the mutation from Val to Ala at P9 of peptide E-247 (DAHAKRQTV), which was found exclusively in microcephaly samples, did not reduce HLA-B8 affinity. In contrast, the mutation from Thr to Pro at P2 of the peptide NS5−832 (VTKWTDIPY) decreased the interaction energy, number of intermolecular interactions, and adversely affected its binding mode with HLA-A1. Overall, our findings are important with regard to the design of T-cell peptide vaccines and for understanding how ZIKV escapes recognition by CD8 + T-cells.     

用分子对接方法研究HIV-1整合酶与病毒DNA的结合模式

用分子对接方法研究了HIV-1整合酶(Integrase, IN)二聚体与3’ 端加工(3’ Processing, 3’-P)前的8 bp及27 bp病毒DNA的相互作用, 并获得IN与27 bp病毒DNA的特异性结合模式. 模拟结果表明, IN有特异性DNA结合区和非特异性DNA结合区; IN二聚体B链的K14, R20, K156, K159, K160, K186, K188, R199和A链的K219, W243, K244, R262, R263是IN结合病毒DNA的关键残基; 并从结构上解释了能使IN发挥活性的病毒DNA的最小长度是15 bp. 通过分析结合能发现, IN与DNA稳定结合的主要因素是非极性相互作用, 而关键残基与病毒DNA相互识别主要依赖于极性相互作用. 模拟结果与实验数据较吻合.     

Molecular mechanics and dynamics study of DNA-furocoumarins complexes: Effect of methylation of the angular derivatives on the intercalation geometry

Summary Results of molecular mechanics calculations on intercalation complexes between DNA and angelicin derivatives: angelicin, 4-methylangelicin, 5-methylangllicin, 4,4-dimethylangelicin, 4,5-dimethylangelicin, 4,6,4-trimethylangelicin and 4,6,5-trimethylangelicin, are presented. The correlation between the presence of methyl groups and an increase in DNA photobinding affinity is discussed on the basis of the molecular structures. The influence of the orientation of the angelicins within the intercalation cavity is also discussed. Finally, the consequences of the dynamical behaviour of angelicin in the intercalation cite are studied.Abbreviations CNDO complete neglect of differential overlap - NMR nuclear magnetic resonance - rms root mean square - UV-A ultraviolet light of class A (320<<400 nm)