Novel antimicrobial peptides based on Protegrin-1: In silico and in vitro assessments.

The development of antibiotic resistance has caused significant health problems. Antimicrobial peptides (AMPs) are considered next-generation antibiotics. Protegrin-1 (PG-1) is a ß-hairpin AMP with a membrane-binding capacity. This study used twelve PG-1 analogs with different amino acid substitutions. Coarse-grained molecular dynamics (MD) simulations were used to assess these analogs, and their physicochemical properties were computed using the Antimicrobial Peptide Database. Three AMPs, PEP-D, PEP-C, and PEP-H, were chosen and synthesized for antibacterial testing. The microbroth dilution technique and hemolytic assays evaluated the antimicrobial efficacy and cellular toxicity. The checkerboard method was used to test the combined activity of AMP and standard antibiotics. Cell membrane permeability and electron microscopy were used to evaluate the mode of action. The chemical stability of the selective AMP, PEP-D, was assessed by a validated HPLC method. PEP-D consists of 16-18 amino acid residues and has a charge of +7 and a hydrophobicity of 44 %, similar to PG-1. It can efficiently inactivate bacteria by disrupting cell membranes and significantly reducing hemolytic activity. Chemical stability studies indicated that AMP was stable at 40 °C for six months under autoclave conditions. This study could introduce the potential therapeutic application of selective AMP as an anti-infective agent.

LPTD: a novel linear programming-based topology determination method for cryo-EM maps.

SUMMARY: Topology determination is one of the most important intermediate steps toward building the atomic structure of proteins from their medium-resolution cryo-electron microscopy (cryo-EM) map. The main goal in the topology determination is to identify correct matches (i.e. assignment and direction) between secondary structure elements (SSEs) (α-helices and ß-sheets) detected in a protein sequence and cryo-EM density map. Despite many recent advances in molecular biology technologies, the problem remains a challenging issue. To overcome the problem, this article proposes a linear programming-based topology determination (LPTD) method to solve the secondary structure topology problem in three-dimensional geometrical space. Through modeling of the protein's sequence with the aid of extracting highly reliable features and a distance-based scoring function, the secondary structure matching problem is transformed into a complete weighted bipartite graph matching problem. Subsequently, an algorithm based on linear programming is developed as a decision-making strategy to extract the true topology (native topology) between all possible topologies. The proposed automatic framework is verified using 12 experimental and 15 simulated α-ß proteins. Results demonstrate that LPTD is highly efficient and extremely fast in such a way that for 77% of cases in the dataset, the native topology has been detected in the first rank topology in <2 s. Besides, this method is able to successfully handle large complex proteins with as many as 65 SSEs. Such a large number of SSEs have never been solved with current tools/methods. AVAILABILITY AND IMPLEMENTATION: The LPTD package (source code and data) is publicly available at https://github.com/B-Behkamal/LPTD. Moreover, two test samples as well as the instruction of utilizing the graphical user interface have been provided in the shared readme file. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

1,2,3,4,6-Pentagalloyl glucose of Pistacia lentiscus can inhibit the replication and transcription processes and viral pathogenesis of SARS-COV-2.

SARS-COV-2 stands as the source of the most catastrophic pandemic of this century, known as COVID-19. In this regard, we explored the effects of five Pistacia sp. active ingredients on the most crucial targets of SARS-COV-2, including 3CLpro, PLpro, RdRp, helicase, NSP15, and E protein. The results of molecular docking determined 1,2,3,4,6-pentagalloyl glucose (PG) as the most effective compound of Pistacia sp, which also confirmed its excellent binding affinities and stable interactions with helicase (-10.76 kcal/mol), RdRp (-10.19 kcal/mol), E protein (-9.51 kcal/mol), and 3CLpro (-9.47 kcal/mol). Furthermore, MD simulation was conducted to investigate the stability of all complexes throughout a 100 ns. In contrast to PLpro and NSP15, the analyses of Lennard-Jones potential, RMSDas, PCA, and SASA verified the ability of PG in forming stable and adequate interactions with RdRp, helicase, 3CLpro, and E protein due to standing as an effective inhibitor among the six targets, these data proposed the capability of PG, the most important compound of Pistacia sp., in inducing antiviral, anti-inflammatory, and antioxidant impacts on RdRp, helicase, 3CLpro, and E protein. Therefore, the possibility of inhibiting the replication and transcription processes and viral pathogenesis of SARS-COV-2 may be facilitated through the application of PG.

Evaluation of the binding effect and cytotoxicity assay of 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione on calf thymus DNA: spectroscopic, calorimetric, and molecular dynamics approaches.

With advances in new drug therapies, it is essential to understand the interactions between drugs and target molecules. In this study, we applied multiple spectroscopic techniques including absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, calorimetric, and molecular dynamics (MD) simulation to study the interaction between 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione (PPF) and calf thymus DNA (ct DNA) in the absence or presence of histone H1. PPF exhibits a high binding affinity towards ct DNA in binary and ternary systems. In addition, the result for the binding constant was observed within the range 104 M-1 achieved through fluorescence quenching data, while the values for enthalpy and entropy changes for ct DNA-PPF and (ct DNA-H1) PPF complexes were measured to be -72.54 kJ.mol-1 , -161.14 J.mol-1  K-1 , -85.34 kJ.mol-1 , and -19.023 J.mol-1  K-1 , respectively. Furthermore, in accordance with circular dichroism spectra, the inducement of ct DNA structural changes was observed during binding of PPF and H1 in binary and ternary system forms. The essential roles of hydrogen bonding and van der Waals forces throughout the interaction were suggested using thermodynamic parameters. According to the obtained data, the interaction mode of ct DNA-PPF and (ct DNA-H1) PPF complexes was intercalation binding. Suggested by the MD simulation study, the ct DNA-H1 complex caused a reduction in the stability of the DNA structure in the presence or absence of ligand, which demonstrated that PPF as an intercalating agent can further distort the structure. The information achieved from this study will be very helpful in understanding the effects of PPF on the conformational state of ct DNA in the absence or presence of the H1 molecule, which seems to be quite significant for clarifying the mechanisms of action and its pharmacokinetics.

Identification of a novel truncating variant in AHI1 gene and a brief review on mutations spectrum.

Joubert syndrome (JS) is a rare inherited neurodevelopmental condition characterized by hypotonia, ataxia, developmental delay, abnormal eye movements, neonatal respiratory disturbance and unique midbrain-hindbrain malformation, known as the molar tooth sign. JS is a genetically heterogeneous disorder with nearly 35 ciliary genes are implicated in its pathogenesis. AHI1 gene is one of the most frequently mutated gene in JS patients which is accounted for 8-11% of cases, particularly in Arab population. AHI1 encodes a cilium-localized protein with a significant role in mediating vesicle trafficking, ciliogenesis and cell polarity. Here, we report a novel pathogenic variant in AHI1 gene and review previously published mutations in AHI1 gene briefly. Whole exome sequencing was employed to determine the causative mutation in an Iranian Arab family with JS from southwestern Iran. Segregation analysis of the candidate variant in the family members was performed using PCR-Sanger sequencing. This approach found a novel homozygous nonsense variant c.832C > T (p.Gln278Ter) in AHI1. Segregation analysis was consistent with individual's phenotype and an autosomal recessive pattern in the family. The variant residing in a relatively highly conserved region and fulfilled the criteria required to be classified as a pathogenic variant based on American College of Medical Genetics and Genomics guidelines. This study confirms the diagnosis of JS in this family and highlights the efficiency of next-generation sequencing-based technique to identify the genetic causes of hereditary disorders with locus heterogeneity.

An Altmetrics Analysis of the Articles Published in the Medical Journal of the Islamic Republic of Iran (1987-2020).

Background: As a newly-emerged metric for evaluating scientific research, altmetrics captures the online activity regarding individual scientific items and is increasingly used in disseminating scientific information in a real-time span. This study aimed to conduct an altmetrics analysis of articles published in the Medical Journal of the Islamic Republic of Iran (MJIRI) during 1987-2020. Methods: Using the archives of MJIRI's articles (during 1987-2020) and the four databases of Google Scholar, Scopus, Dimensions, and Altmetrics needed data on received citations as well as altmetric indicators and altmetric attention scores of these articles were extracted manually in December 2020. Data analysis was done in Excell and SPSS-25. Results: Only 1274 MJIRI articles (about 51%) were present in the Altmetric Institute and had an altmetric attention score. Only 109 papers (8.5%) were shared at least once on online social media. Twitter was the most frequent social medium used for sharing the articles (n=91, 7.14%). These articles were twitted 171 times in total and the mean rate of twitting them was 1.88 per paper. Users from 21 countries in the world tweeted the articles. The top three twitting courtiers/regions were the United States (n=47), the United Kingdom (n=14) and India (n=3), respectively. Regarding twitters' membership status, the top three ranks were dedicated to the members of the public with 137 twits, practitioners (doctors and other healthcare professionals) with 18 twits and scientists with 16 twits. In Mendeley, the top three ranks were dedicated to master students (n=284), bachelor students (n=240) and Ph.D. students (n=155), respectively. The top three disciplines in this regard were medicine and dentistry (n=335), nursing and health profession (n=190), and biochemistry, genetics and molecular biology (n=68). Most of the highly-mentioned articles were review papers. The relationship between the altmetric attention score and citation performance of MJIR articles was not significant (p>0.05). Conclusion: This study is one of the first studies to investigate the altmetrics indicators of articles published in an Iranian high-prestigious internationally-wide medical journal. Using social media tools can certainly promote medical scholars' scientific interactions and make added value for research published in medical journals. Editorial boards, including that of MJIRI can use altmetrics for detecting research trends and publishing approaches and consequently increased citation counts and research impact.

Iranian researchers' contributions to research on COVID-19: A bibliometric analysis and visualization.

Background: COVID-19 pandemic crisis motivated researchers worldwide to deeply investigate it from different perspectives. As Iran is one of the highly-affected countries by Covid-19, Iranian researchers have focused on studying it. This study aimed at analyzing and visualizing Iranian researchers' papers on COVID-19 from a bibliometric perspective. Methods: By searching MeSH-selected keywords related to COVID-19 in Scopus, Iranian researchers' papers on COVID-19 were extracted in a CSV format and underwent bibliometric techniques, such as coauthorship analysis, citation, and co-citation analysis, keyword and term co-occurrence mapping and etc. in the Microsoft Excel and VOSviewer software package. Results: A total of 405 papers were authored by Iranian researchers on COVID-19 during the study period, with the average number of citations per paper of 2.60 and a mean h-index of 15. The majority of papers were original articles in English. Archives of Clinical Infectious Diseases and Archives of Iranian Medicine and Medical Hypotheses were highly ranked publishing journals, respectively. The most productive institute and author were Tehran University of Medical Sciences with 119 papers and Rezaei, N. with 12 papers. Iranian researchers collaborated with the researchers of 73 countries, with the USA ranking first in Covid-19 research, followed by Italy, Canada, and United Kingdom. In publishing papers on COVID-19, Iran ranked first among the Middle Eastern countries and thirteenth internationally. Conclusion: Iranian researchers were active in 5 main areas of COVID-19 research, including epidemiology, diagnosis, treatment, virology, and systematic review.

Information Technology-Based Interventions to Improve Drug-Drug Interaction Outcomes: A Systematic Review on Features and Effects.

The purpose of this systematic review was to identify features and effects of information technology (IT)-based interventions on outcomes related to drug-drug interactions (DDI outcomes). A literature search was conducted in Medline, EMBASE, and the Cochrane Library for published English-language studies. Studies were included if a main outcome was related to DDIs, the intervention involved an IT-based system, and the study design was experimental or observational with controls. Study characteristics, including features and effects of IT-based interventions, were extracted. Nineteen studies comprising five randomized controlled trials (RCT), five non-randomized controlled trials (NRCT) and nine observational studies with controls (OWC) were included. Sixty-four percent of prescriber-directed interventions, and all non-prescriber interventions, were effective. Each of the following characteristics corresponded to groups of studies of which a majority were effective: automatic provision of recommendations within the providers' workflow, intervention at the time of decision-making, integration into other systems, and requiring the reason for not following the recommendations. Only two studies measured clinical outcomes: an RCT that showed no significant improvement and an OWC that showed improvement, but did not statistically assess the effect. Most studies that measured surrogate outcomes (e.g. potential DDIs) and other outcomes (e.g. adherence to alerts) showed improvements. IT-based interventions improve surrogate clinical outcomes and adherence to DDI alerts. However, there is lack of robust evidence about their effectiveness on clinical outcomes. It is recommended that researchers consider the identified features of effective interventions in the design of interventions and evaluate the effectiveness on DDI outcomes, particularly clinical outcomes.

Comparison of the binding behavior of FCCP with HSA and HTF as determined by spectroscopic and molecular modeling techniques.

The interaction of carbonylcyanide p-(trifluoromethoxy) phenylhydrazone (FCCP) with human serum albumin (HSA) and human transferrin (HTF) was investigated using multiple spectroscopy, molecular modeling, zeta-potential and conductometry measurements of aqueous solutions at pH 7.4. The fluorescence, UV/vis and polarization fluorescence spectroscopy data disclosed that the drug-protein complex formation occurred through a remarkable static quenching. Based on the fluorescence quenching, two sets of binding sites with distinct affinities for FCCP existed in the two proteins. Steady-state and polarization fluorescence analysis showed that there were more affinities between FCCP and HSA than HTF. Far UV-CD and synchronous fluorescence studies indicated that FCCP induced more structural changes on HSA. The resonance light scattering (RLS) and zeta-potential measurements suggested that HTF had a greater resistance to drug aggregation, whereas conductometry measurements expressed the presence of free ions improving the resistance of HSA to aggregation. Thermodynamic measurements implied that a combination of electrostatic and hydrophobic forces was involved in the interaction between FCCP with both proteins. The phase diagram plots indicated that the presence of second binding site on HSA and HTF was due to the existence of intermediate structures. Site marker competitive experiments demonstrated that FCCP had two distinct binding sites in HSA which were located in sub-domains IIA and IIIA and one binding site in the C-lobe of HTF as confirmed by molecular modeling. The obtained results suggested that both proteins could act as drug carriers, but that the HSA potentially had a higher capacity for delivering FCCP to cancerous tissues.

Spectroscopy and molecular simulation on the interaction of Nano-Kaempferol prepared by oil-in-water with two carrier proteins: An investigation of protein-protein interaction.

In this work, the interaction of human serum albumin (HSA) and human holo-transferrin (HTF) with the prepared Nano-Kaempferol (Nano-KMP) through oil-in-water procedure was investigated in the form of binary and ternary systems by the utilization of different spectroscopy techniques along with molecular simulation and cancer cell experiments. According to fluorescence spectroscopy outcomes, Nano-KMP is capable of quenching both proteins as binary systems by a static mechanism, while in the form of (HSA-HTF) Nano-KMP as the ternary system, an unlinear Stern-Volmer plot was elucidated with the occurrence of both dynamic and static fluorescence quenching mechanisms in the binding interaction. In addition, the two acquired Ksv values in the ternary system signified the existence of two sets of binding sites with two different interaction behaviors. The binding constant values of HSA-Nano KMP, HTF-Nano-KMP, and (HSA-HTF) Nano-KMP complexes formation were (2.54 ± 0.03) × 104, (2.15 ± 0.02) × 104 and (1.43 ± 0.04) × 104M-1at the first set of binding sites and (4.68 ± 0.05) × 104 M-1 at the second set of binding sites, respectively. The data of thermodynamic parameters confirmed the major roles of hydrogen binding and van der Waals forces in the formation of HSA-Nano KMP and HTF-Nano KMP complexes. The thermodynamic parameter values of (HSA-HTF) Nano KMP revealed the dominance of hydrogen binding and van der Waals forces in the first set of binding sites and hydrophobic forces for the second set of binding sites. Resonance light scattering (RLS) analysis displayed the existence of a different interaction behavior for HSA-HTF complex in the presence of Nano-KMP as the ternary system. Moreover, circular dichroism (CD) technique affirmed the conformational changes of the secondary structure of proteins as binary and ternary systems. Molecular docking and molecular dynamics simulations (for 100 ns) were performed to investigate the mechanism of KMP binding to HSA, HTF, and HSA-HTF. Next to observing a concentration and time-dependent cytotoxicity, the down regulation of PI3K/AkT/mTOR pathway resulted in cell cycle arrest in SW480 cells.

New Perspective on the Interaction Behavior Between Riboflavin and ß Lactoglobulin-ß Casein Complex by Biophysical Techniques.

Riboflavin (RF) is a vitamin that only exists in plants and microorganisms and must be procured externally by humans. On the other hand, there are two major allergic factors in cow's milk, including ß-lactoglobulin (ßLG) and ß-casein (ßCN), while their allergic properties can be eliminated by binding to micronutrients. In this regard, we examined the binding process of RF to ßLG and ßCN in the binary and ternary systems by different spectroscopies such as zeta potential, electric conductivity, and molecular modeling. According to the result of the fluorescence spectrum regarding the interaction of RF with ßLG and ßCN in binary and ternary systems, an increase in RF concentration declined the fluorescence intensity of three systems and also caused the quenching of proteins. Static quenching plays a pivotal role in the formation of stable interactions. The obtained thermodynamic parameters by Van't Hoff equation ascertained the predominance of hydrogen bonds and van der Waals interaction in all the systems. Considering how the negative value of ΔH0 resulted in the negative value of ΔG0, the systems were assumed to be enthalpy driven. The outcomes of circular dichroism (CD) disclosed that the attachment of RF to the targets of systems increased their a-helix content, which particularly included the binding of RF to ßLG that led to the conversion of ß-sheet to α-helix content. As indicated by the results of zeta potential, the low concentration of RF contained the dominance of hydrophobic forces in the interactions, whereas the enlargement of this concentration prevailed electrostatic forces. Moreover, conductometry measurements showed an extension in the rate of ionizable groups due to the addition of RF to the systems, which may increase the probability of an interaction between RF, ßCN, and ßLG in binary and ternary systems. In consistency with the outcomes of molecular dynamics simulation, the data of molecular docking approved the capability of RF in forming strong and stable interactions with ßCN and ßLG.

Targeted delivery of SN38 to breast cancer using amphiphilic diblock copolymers PHPMA-b-PBAEM as micellar carriers with AS1411 aptamer.

Breast cancer treatment can be challenging, but a targeted drug delivery system (DDS) has the potential to make it more effective and reduce side effects. This study presents a novel nanotherapeutic targeted DDS developed through the self-assembly of an amphiphilic di-block copolymer to deliver the chemotherapy drug SN38 specifically to breast cancer cells. The vehicle was constructed from the PHPMA-b-PEAMA diblock copolymer synthesized via RAFT polymerization. A single emulsion method was then used to encapsulate SN38 within nanoparticles (NPs) formed from the PHPMA-b-PEAMA copolymer. The AS1411 DNA aptamer was covalently bonded to the surface of the micellar NPs, producing a targeted DDS. Molecular dynamics (MD) simulation studies were also performed on the di block polymeric system, demonstrating that SN38 interacted well with the di block. The in vitro results demonstrated that AS1411- decorated SN38-loaded HPMA NPs were highly toxic to breast cancer cells while having a minimal effect on non-cancerous cells. Remarkably, in vivo studies elucidated the ability of the targeted DDS to enhance the antitumor effect of SN38, suppressing tumor growth and improving survival rates compared to free SN38.

Investigation on the interaction between cyclophosphamide and lysozyme in the presence of three different kind of cyclodextrins: determination of the binding mechanism by spectroscopic and molecular modeling techniques.

The interactions between cyclophosphamide (CYC) and lysozyme (LYZ) in the presence of different cyclodextrins (CDs) were investigated by UV absorption, fluorescence spectroscopy, circular dichroism (CD), and molecular modeling techniques under imitated physiological conditions. The UV absorption results showed the formation of complexes between CYC and LYZ in the presence of different CDs. Fluorescence data show that CYC has a stronger quenching effect on LYZ, and the red shifts suggested that the microenvironment of Trp residues was changed and became more hydrophilic. The interaction of CYC with LYZ and quenching properties of the complexes caused strong static fluorescence quenching in binary and ternary systems. The binding affinities as well as the number of binding sites were obtained from interaction between CYC and LYZ in the presence of different CDs as binary and ternary systems by modified Stern-Volmer plots. The Resonance Light Scattering (RLS) technique was utilized to investigate the effect of drug and CDs on conformational changes of LYZ as separate and simultaneous. The results suggested that the enhancement of RLS intensity was attributed to the formation of a complex between drug and protein in absence and presence of CDs. The effect of CYC and cyclodextrins on the conformation of LYZ was analyzed using synchronous fluorescence spectroscopy. Our results revealed that the fluorescence quenching of LYZ originated from the Trp and Tyr residues, and demonstrated conformational changes of LYZ with the addition of CYC and CDs. The molecular distances between the donor (LYZ) and acceptor (CYC and CDs) in binary and ternary systems were estimated according to Forster's theory and showed static quenching for protein with CYC in the presence of CDs. The CD spectra indicated that the binding of the CYC induced secondary structural changes in LYZ in binary and ternary systems. Molecular modeling suggested the binding sites of CYC in the ternary systems differ from those in the binary systems. estimated the distance between CYC and Trp residues in binary and ternary systems in the presence of CDs and confirmed the experimental results.

Endogenous enzymatic antioxidant status of whiteleg shrimp (Litopenaeus vannamei) following exposure to sublethal concentrations of silver nanoparticles.

Immunotoxicity of silver nanoparticles (AgNPs) to whiteleg shrimp (Litopenaeus vannamei) was assessed using redox-status orchestrating enzymes. To this end, the shrimp was exposed to sublethal AgNPs concentrations (0 % LC50: control; 25 % LC50: 0.97 mg/L; 50 % LC50: 1.95 mg/L; 75 % LC50: 2.92 mg/L). During the experiment, the behavior of superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), and glutathione peroxidase (GPx) was monitored, besides total antioxidant capacity (TAC) and malondialdehyde (MDA). The hepatopancreas SOD activity reduced about 63 %-76 % at.%50 LC50 and %75 LC50 AgNPs treatments, and CAT decreased in both tissues at 50 % LC50 AgNPs. TAC exhibited a U-form response in the hepatopancreas organ against stress caused by AgNPs, and hepatopancreas MDA displayed a time-dependent increase. Taken together, AgNPs triggered severe immunotoxicity through suppression of CAT, SOD, and TAC in the hepatopancreas tissue.

Discovery of New Ligand with Quinoline Scaffold as Potent Allosteric Inhibitor of HIV-1 and Its Copper Complexes as a Powerful Catalyst for the Synthesis of Chiral Benzimidazole Derivatives, and in Silico Anti-HIV-1 Studies.

In this paper, the novel Schiff base ligand containing quinoline moiety and its novel copper chelate complexes were successfully prepared. The catalytic activity of the final complex in the organic reaction such as synthesis of chiral benzimidazoles and anti-HIV-1 activity of Schiff base ligand and the products of this reaction were investigated. In addition, green chemistry reactions using microwaves, powerful catalyst synthesis, green recovery and reusability, and separation of products with economic, safe, and clean methods (green chemistry) are among the advantages of this protocol. The potency of these compounds as anti-HIV-1 agents was investigated using molecular docking into integrase (IN) enzyme with code 1QS4 and the GROMACS software for molecular dynamics simulation. The final steps were evaluated in case of RMSD, RMSF, and Rg. The results revealed that the compound VII exhibit a good binding affinity to integrase (Δg = -10.99 kcal/mol) during 100 ns simulation time, and the analysis of RMSD suggested that compound VII was stable in the binding site of integrase.

Exploring the binding behavior mechanism of vitamin B12 to α-Casein and ß-Casein: multi-spectroscopy and molecular dynamic approaches.

The aim of this study was to investigate the behavior interaction of α-Casein-B12 and ß-Casein-B12 complexes as binary systems through the methods of multiple spectroscopic, zeta potential, calorimetric, and molecular dynamics (MD) simulation. Fluorescence spectroscopy denoted the role ofB12as a quencher in both cases of α-Casein and ß-Casein fluorescence intensities, which also verifies the existence of interactions. The quenching constants of α-Casein-B12 and ß-Casein-B12 complexes at 298 K in the first set of binding sites were 2.89 × 104 and 4.41 × 104 M-1, while the constants of second set of binding sites were 8.56 × 104 and 1.58 × 105 M-1, respectively. The data of synchronized fluorescence spectroscopy at Δλ = 60 nm were indicative of the closer location of ß-Casein-B12 complex to the Tyr residues. Additionally, the binding distance between B12 and the Trp residues of α-Casein and ß-Casein were obtained in accordance to the Förster's theory of nonradioactive energy transfer to be 1.95 nm and 1.85 nm, respectively. Relatively, the RLS results demonstrated the production of larger particles in both systems, while the outcomes of zeta potential confirmed the formation of α-Casein-B12 and ß-Casein-B12 complexes and approved the existence of electrostatic interactions. We also evaluated the thermodynamic parameters by considering the fluorescence data at three varying temperatures. According to the nonlinear Stern-Volmer plots of α-Casein and ß-Casein in the presence of B12 in binary systems, the two sets of binding sites indicated the detection of two types of interaction behaviors. Time-resolved fluorescence results revealed that the fluorescence quenching of complexes are static mechanism. Furthermore, the outcomes of circular dichroism (CD) represented the occurrence of conformational changes in α-Casein and ß-Casein upon their binding to B12 as the binary system. The experimental results that were obtained throughout the binding of α-Casein-B12 and ß-Casein-B12 complexes were confirmed by molecular modeling.Communicated by Ramaswamy H. Sarma.

Structure, Function, and Physicochemical Properties of Pore-forming Antimicrobial Peptides.

Antimicrobial peptides (AMPs), a class of antimicrobial agents, possess considerable potential to treat various microbial ailments. The broad range of activity and rare complete bacterial resistance to AMPs make them ideal candidates for commercial development. These peptides with widely varying compositions and sources share recurrent structural and functional features in mechanisms of action. Studying the mechanisms of AMP activity against bacteria may lead to the development of new antimicrobial agents that are more potent. Generally, AMPs are effective against bacteria by forming pores or disrupting membrane barriers. The important structural aspects of cytoplasmic membranes of pathogens and host cells will also be outlined to understand the selective antimicrobial actions. The antimicrobial activities of AMPs are related to multiple physicochemical properties, such as length, sequence, helicity, charge, hydrophobicity, amphipathicity, polar angle, and also self-association. These parameters are interrelated and need to be considered in combination. So, gathering the most relevant available information will help to design and choose the most effective AMPs.

Understanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison.

The interaction between calf thymus DNA (ctDNA) and Malathion in the absence and presence of Histone 1 has been enquired by the means of spectroscopic, viscometry, molecular modeling, and cell viability assay techniques. Malathion is capable of quenching the fluorescence of ct DNA in the absence and presence of H1. The binding constants of Malathion-ctDNA complex in the absence of H1 have been calculated to be 6.62 × 104, 4.31 × 104 and 1.93 × 104 M-1 at 298, 303, and 308 K, respectively that revealed static quenching in complex formation. The observed negative values of enthalpy and entropy changes indicate that the main binding interaction forces were van der Waals force and hydrogen bonding. The binding constant between Malathion and single-stranded ctDNA (ss ctDNA) seemed to be much weaker than that of Malathion and double-stranded ctDNA (ds ctDNA). Furthermore, Malathion can induce detectable alterations in the CD spectrum of ctDNA, along with changes in its viscosity. In the presence of H1, fluorescence quenching of ctDNA-Malathion complex displays dynamic behavior and binding constants were perceived to be 1.66 × 104, 2.93 × 104 and 5.77 × 104 M-1 at 298, 303, and 308 K, respectively. The different of interaction behavior between ctDNA and Malathion in the absence and presence of H1 clearly revealed H1 role in the complex formation and forces change between ctDNA and Malathion. The positive values of enthalpy and entropy changes have suggested that binding process is primarily driven by hydrophobic interactions. The tendency to interact with ss ctDNA, reduced viscosity have designated that the Malathion bound to ctDNA in the presence of H1 is groove binding. The results of molecular docking and molecular dynamics simulation also confirmed potent interactions between Malathion and the macromolecules in the binary and ternary systems.Communicated by Ramaswamy H. Sarma.

Multi spectroscopic and molecular simulation studies of propyl acridone binding to calf thymus DNA in the presence of electromagnetic force.

Introduction: Here, the interaction behavior between propyl acridones (PA) and calf thymus DNA (ct-DNA) has been investigated to attain the features of the binding behavior of PA with ct-DNA, which includes specific binding sites, modes, and constants. Furthermore, the effects of PA on the conformation of ct-DNA seem to be quite significant for comprehending the medicine's mechanism of action and pharmacokinetics. Methods: The project was accomplished through means of absorbance studies, fluorescence spectroscopy, circular dichroism, viscosity measurement, thermal melting, and molecular modeling techniques. Results: The intercalation of PA has been suggested by fluorescence quenching and viscosity measurements results while the thermal melting and circular dichroism studies have confirmed the thermal stabilization and conformational changes that seem to be associated with the binding. The binding constants of ct-DNA-PA complex, in the absence and presence of EMF, have been evaluated to be 6.19 × 104 M-1 and 2.95 × 104 M-1 at 298 K, respectively. In the absence of EMF, the ∆H0 and ∆S0 values that occur in the interaction process of PA with ct-DNA have been measured to be -11.81 kJ.mol-1 and 51.01 J.mol-1K-1, while in the presence of EMF they were observed to be -23.34 kJ.mol-1 and 7.49 J.mol-1K-1, respectively. These numbers indicate the involvement of multiple non-covalent interactions in the binding procedure. In a parallel study, DNA-PA interactions have been monitored by molecular dynamics simulations; their results have demonstrated DNA stability with increasing concentrations of PA, as well as calculated bindings of theoretical ΔG0. Conclusion: The complex formation between PA and ct-DNA has been investigated in the presence and absence of EMF through the multi spectroscopic techniques and MD simulation. These findings have been observed to be parallel to the results of KI and NaCl quenching studies, as well as the competitive displacement with EB and AO. According to thermodynamic parameters, electrostatic interactions stand as the main energy that binds PA to ct-DNA. Regarding the cases that involve the Tm of ct-DNA, EMF has proved to increase the stability of binding between PA and ct-DNA.

Amino acid-mPEGs: Promising excipients to stabilize human growth hormone against aggregation.

Objectives: Today, the non-covalent PEGylation methods of protein pharmaceuticals attract more attention and possess several advantages over the covalent approach. In the present study, Amino Acid-mPEGs (aa-mPEGs) were synthesized, and the human Growth Hormone (hGH) stability profile was assessed in their presence and absence. Materials and Methods: aa-mPEGs were synthesized with different amino acids (Trp, Glu, Arg, Cys, and Leu) and molecular weights of polymers (2 and 5 KDa). The aa-mPEGs were analyzed with different methods. The physical and structural stabilities of hGH were analyzed by SEC and CD spectroscopy methods. Physical stability was assayed at different temperatures within certain intervals. Molecular dynamics (MD) simulation was used to realize the possible mode of interaction between protein and aa-mPEGs. The cell-based method was used to evaluate the cytotoxicity. Results: HNMR and FTIR spectroscopy indicated that aa-mPEGs were successfully synthesized. hGH as a control group is known to be stable at 4 °C; a pronounced change in monomer degradation is observed when stored at 25 °C and 37 °C. hGH:Glu-mPEG 2 kDa with a molar ratio of 1:1 to the protein solution can significantly increase the physical stability. The CD spectroscopy method showed that the secondary structure of the protein was preserved during storage. aa-mPEGs did not show any cytotoxicity activities. The results of MD simulations were in line with experimental results. Conclusion: This paper showed that aa-mPEGs are potent excipients in decreasing the aggregation of hGH. Glu-mPEG exhibited the best-stabilizing properties in a harsh environment among other aa-mPEGs.