What in silico molecular docking can do for the ‘bench-working biologists’

Structure-Based Drug Design for Targeting IRE1: An in Silico Approach for Treatment of Cancer

BACKGROUND

Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) play a key role in cancer progression. The aggregation of incorrectly folded proteins in the ER generates ER stress, which in turn activates the UPR as an adaptive mechanism to fix ER proteostasis. Inositol-requiring enzyme 1 (IRE1) is the most evolutionary conserved ER stress sensor, which plays a pro-tumoral role in various cancers. Targeting its' active sites is one of the most practical approaches for the treatment of cancers.

OBJECTIVE

In this study, we aimed to use the structure of 4μ8C as a template to produce newly designed compounds as IRE1 inhibitors.

METHODS

Various functional groups were added to the 4μ8C, and their binding affinity to the target sites was assessed by conducting a covalent molecular docking study. The potential of the designed compound for further in vitro and in vivo studies was evaluated using ADMET analysis.

RESULTS

Based on the obtained results, the addition of hydroxyl groups to 4μ8C enhanced the binding affinity of the designed compound to the target efficiently. Compound 17, which was constructed by the addition of one hydroxyl group to the structure of 4μ8C, can construct a strong covalent bond with Lys907. The outcomes of ADMET analysis indicated that compound 17 could be considered a drug-like molecule.

CONCLUSION

Our results revealed that designed compound 17 could inhibit IRE1 activity. Therefore, this designed compound is a remarkable inhibitor of IRE1 and introduces a promising therapeutic strategy for cancer treatment.

Anti-collagenase, Anti-elastase, Anti-urease, and Anti-cancer Potentials of Isokaempferide as Natural Compound: In vitro and in silico Study

One of the main goals of medicinal chemistry in recent years has been the development of new enzyme inhibitors and anti-cancer medicines. The isokaempferide' ability to inhibit the enzymes urease, elastase, and collagenase were also studied. The results showed that isokaempferide was the most effective compound against the assigned enzymes, with IC 50 values of 23.05 µM for elastase, 12.83 µM for urease, and 33.62 µM for collagenase respectively. It should be emphasized that natural compound was more effective at inhibiting some enzymes. Additionally, the compound was tested for their anti-cancer properties using colon, lung, breast cancer cell lines. The chemical activities of isokaempferide against urease, collagenase, and elastase were investigated utilizing the molecular docking study. The anti-cancer activities of the compound were evaluated against lung cancer cells such as SPC-A-1, SK-LU-1, 95D, breast cancer cells like MCF7, Hs 578Bst, Hs 319.T, and UACC-3133 cell lines, and colon cancer cell lines like CL40, SW1417, LS1034, and SW480. The chemical activities of isokaempferide against some of the expressed surface receptor proteins (EGFR, estrogen receptor, CD47, progesterone receptor, folate receptor, CD44, HER2, CD155, CXCR4, CD97, and endothelin receptor) in the mentioned cell lines were assessed using the molecular docking calculations. The results showed the probable interactions and their characteristics at an atomic level. The docking scores revealed that isokaempferide has a strong binding affinity to the enzymes and proteins. In addition, the compound formed powerful contact with the enzymes and receptors. Thus, isokaempferide could be potential inhibitor for enzymes and cancer cells.

Therapeutic properties, biological effects, antiliver cancer, and anticolon cancer effects of some natural compounds: A biochemical approach

Natural compounds, such as carotenoids, flavonoids, anthocyanins, or terpenoids, are physiologically active components found in plants (pigments), often known as phytochemicals or phytonutrients. The in vitro cytotoxic and anticolon cancer effects of biologically bavachin, bavachinin, artepillin C, and aromadendrin compounds against SW48, SNU-C1, COLO 205, RKO, LS411N, and SW1417 cancer cell lines were assessed. Results of enzymes and antibacterial, antifungal were in level of micromolar that is good impacts. These natural compounds may be antidiabetic, anticancer, and antibacterial candidates for drug design. IC50 results were obtained between 14-19 and 5-119 µM for α-amylase and α-glucosidase, respectively. Good inhibitor Bavachinin was detected for both enzymes (IC50 for α-amylase: 14.37 µM and IC50 for α-glucosidase: 5.27 µM). The chemical activities of aromadendrin, artepillin C, bavachin, and bavachinin against pancreatic α-amylase and α-glucosidase were assessed by conducting the molecular docking study. The chemical activities of aromadendrin, artepillin C, bavachin, and bavachinin against some of the expressed surface receptor proteins (CD44, CD47, CXCR4, EGFR, folate receptor, HER2, and endothelin receptor) in the mentioned cell lines were investigated using the molecular docking calculations. The results illustrated the atomic-level properties and potential interactions. These chemicals have high binding affinities to the enzymes and proteins, according to the docking scores. In addition, the compounds formed strong contacts with the enzymes and receptors. Thus, these compounds could be potential inhibitors for enzymes and cancer cells.

Anticancer and Biological Effects of Some Natural Compounds and Theoretical Investigation of them Against RdRP of SARS-COV-2: In Silico and In Vitro Studies

In this study, Skullcapflavone I and Skullcapflavone II molecules showed good inhibitory activities against α-glucosidase and sorbitol dehydrogenase enzymes with IC50 values of 102.66 ± 8.43 and 95.04 ± 11.52 nM for α-glucosidase and 38.42 ± 3.82 and 28.81 ± 3.26 µM for sorbitol dehydrogenase. The chemical activities of Skullcapflavone I and Skullcapflavone II against α-glucosidase and sorbitol dehydrogenase were assessed by conducting the molecular docking study. The anticancer activities of the compounds were examined against SW-626, SK-OV-3, OVCAR3, and Caov-3 cell lines. The chemical activities of Skullcapflavone I and Skullcapflavone II against some of the expressed surface receptor proteins (estrogen receptor, EGFR, androgen receptor, and GnRH receptor) in the mentioned cell lines were investigated using in silico calculations. Moreover, the activity of the compounds against RNA polymerase of SARS-COVE-2 was also assessed using the molecular modeling study. These compounds created strong contacts with the enzymes and receptors. The considerable binding affinity of the compounds to the enzymes and proteins showed their ability as inhibitors. Furthermore, even at modest dosages, these substances markedly reduced the viability of ovarian cancer cells. Additionally, the viability of ovarian cancer cells was significantly decreased by a 300 μM dosage of all compounds. Antiovarian cancer results of Skullcapflavone I on SK-OV-3, SW-626, OVCAR3, and Caov-3 were 63.14, 1.55, 19.42, and 52.04 µM, respectively. Also, cytotoxicity results of Skullcapflavone II on SK-OV-3, SW-626, OVCAR3, and Caov-3 were 5.18, 21.44, 33.87, and 72.66 µM, respectively.

The anti-melanogenic properties of Swietenia macrophylla king

Fair flawless skin is the goal for some cultures and the development of irregular skin pigmentation is considered an indication of premature skin aging. Hence, there is a rising demand for skin whitening cosmetics. Thus, this research will be focusing on discovering the anti-pigmentation properties of Swietenia macrophylla seeds. Firstly, the seeds were extracted with ethanol and further fractionate based on their polarity before testing them on zebrafish embryos. The ethanolic extract of the seed demonstrated significant inhibition of both tyrosinase activity and melanin production in the embryos. However, after fractionation, the anti-melanogenic ability was observed to have decreased, signifying that the phytocompounds may be synergistic in nature. Still in the proteomic studies the ethanolic extract and its hexane fraction both induced the downregulation of cathepsin LB and cytoskeletal proteins that have connections to the melanogenic pathway, confirming that S. macrophylla seeds do indeed have anti-pigmentation properties that can be exploited for cosmetic use. Next, limonoids (tetranortriterpenoids found in the seed) were tested for their inhibitory effect against human tyrosinase related protein 1 (TYRP-1) via molecular docking. It was found that limonoids have a stronger binding affinity to TYRP-1 than kojic acid, suggesting that these phytocompounds may have the potential in inhibiting pigmentation. However, this still needs further confirmation before these phytocompounds can be developed into a skin whitening agent. Other assays like ex-vivo or 3D human skin culture can also be used to better study the seeds anti-pigmentation effect on humans.

Anti-cancer, Anti-collagenase and Anti-elastase Potentials of Some Natural Derivatives: In vitro and in silico Studies

The anti-cancer activities of the compounds were evaluated against KYSE-150, KYSE-30, and KYSE-270 cell lines and also on investigated esophageal line HET 1 A as a standard. Modified inhibitory impact on enzymes of collagenase and elastase were used Thring and Moon methods, respectively. Among both compounds, both of them recorded impact on cancer cells being neutral against the control, both had IC50 lower than 100 µM and acted as a potential anticancer drug. The chemical activities of Skullcapflavone I and Skullcapflavone II against elastase and collagenase were investigated utilizing the molecular modeling study. IC50 values of Skullcapflavone I and Skullcapflavone II on collagenase enzyme were obtained 106.74 and 92.04 µM and for elastase enzyme were 186.70 and 123.52 µM, respectively. Anticancer effects of these compounds on KYSE 150, KYSE 30, and KYSE 270 esophageal cancer cell lines studied in this work. For Skullcapflavone I, IC50 values for these cell lines were obtained 14.25, 19.03, 25.10 µM, respectively. Also, for Skullcapflavone II were recorded 20.42, 34.17, 22.40 µM, respectively. The chemical activities of Skullcapflavone I and Skullcapflavone II against some of the expressed surface receptor proteins (CD44, EGFR, and PPARγ) in the mentioned cell lines were assessed using the molecular docking calculations. The calculations showed the possible interactions and their characteristics at an atomic level.

Bioactivity of hamamelitannin, flavokawain A, and triacetyl resveratrol as natural compounds: Molecular docking study, anti‐colon cancer and anti‐Alzheimer potentials

In this study, we worked on anticolon cancer effects and anti-Alzheimer's disease with molecular docking studies. Hamamelitannin, flavokawain A, and triacetyl resveratrol compounds showed good inhibitory activities on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes. The inhibition effects of flavokawain A, hamamelitannin, and triacetyl resveratrol on AChE and BuChE enzymes were determined spectrophotometrically conforming to Ellman. IC₅₀ values of these enzymes were ranging between 0.95 ± 0.12 and 93.27 ± 8.14 nM for AChE and 5.71 ± 0.77 and 52.10 ± 8.41 nM for BuChE. The inhibitory activities of some chemical compounds such as flavokawain A, hamamelitannin, and triacetyl resveratrol were assessed by performing the molecular docking study in the presence of AChE and BuChE. Also, the features of the ligand-enzyme complex had value of -7.722 kcal/mol for flavokawain A against AChE and -5.530 kcal/mol against BuChE. The molecular docking calculations indicated the probable interactions and their characteristics at an atomic level. Due to the outcomes gained from docking, the affinity of the chemical compounds to the enzymes was considerable. In vitro cell viabilities of flavokawain A, hamamelitannin, and triacetyl resveratrol with various concentrations on SW620, DLD-1, HT29, HCT8, and HCT116 were investigated by MTT assay with Doxorubicin as the control compound.

Anti-breast Adenocarcinoma and Anti-urease Anti-tyrosinase Properties of 5-Pentylresorcinol as Natural Compound with Molecular Docking Studies

5-Pentylresorcinol is a type of the group of resorcinol compounds that is resorcinol in that has hydrogen atom at position 5 is replaced by a pentyl group. It has a role as a lichen metabolite. This compound showed excellent to good inhibitory activities against studied these enzymes with IC₅₀ values of 65.96 µM for urease and 34.81 µM for tyrosinase. Standard compounds for enzymes had IC₅₀ values of 1.94±0.24 µM against urease and 84.36±5.17 µM against tyrosinase. The IC₅₀ of 5-pentylresorcinol against MCF7 cell line was 165.72 µg/mL; against Hs 578Bst cell line was 102.14 µg/mL; against Hs 319.T cell line was 12.34 µg/mL; and against UACC-3133 cell line was 73.07 µg/mL, respectively. The chemical activities of 5-pentylresorcinol against urease and tyrosinase were evaluated using the molecular modeling study. The anti-cancer activity of 5-pentylresorcinol was also investigated by treating the compound on the BRCT repeat region from the breast cancer-associated protein (BRCA1), and their interactions were assessed utilizing the molecular docking calculations. The results revealed the probable interactions and their characteristics at an atomic level. The docking scores of 5-pentylresorcinol against urease, tyrosinase, and BRCA1 are -3.073, -5.262, and -3.238 (kcal/mol), respectively.

Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators

Molecular dynamics (MD) simulations allow researchers to investigate the behavior of desired biological targets at ever-decreasing costs with ever-increasing precision. Among the biological macromolecules, ion channels are remarkable transmembrane proteins, capable of performing special biological processes and revealing a complex regulatory matrix, including modulation by small molecules, either endogenous or exogenous. Recently, given the developments in ion channel structure determination and accessibility of bio-computational techniques, MD and related tools are becoming increasingly popular in the intense research area regarding ligand-channel interactions. This review synthesizes and presents the most important fields of MD involvement in investigating channel-molecule interactions, including, but not limited to, deciphering the binding modes of ligands to their ion channel targets and the mechanisms through which chemical compounds exert their effect on channel function. Special attention is devoted to the importance of more elaborate methods, such as free energy calculations, while principles regarding drug design and discovery are highlighted. Several technical aspects involving the creation and simulation of channel-molecule MD systems (ligand parameterization, proper membrane setup, system building, etc.) are also presented.

Artemisinin Derivatives Target Topoisomerase 1 and Cause DNA Damage in Silico and in Vitro

DNA topoisomerases 1 and 2 are enzymes that maintain DNA topology and play important essential genome functions, including DNA replication and transcription. Aberrant topoisomerases cause genome instability and a wide range of diseases, cancer in particular. Both Topo 1 and 2 are the targets of valuable anticancer drugs, such as camptothecin. It has been previously shown that artemisinin, a sesquiterpene lactone from Artemisia annua L. also known as qinghaosu, possesses anti-cancer effects and one of its derivatives, artesunate inhibits Topo 2. In this study, we evaluated artemisinin and 40 derivatives as potential Topo 1 inhibitors at first by in silico molecular docking analyses. Five compounds that showed comparable binding energies and similar docking poses were selected for in vitro cytotoxicity test and Comet assay for DNA damage. WWLL-013, WWLL-022, and WWLL-1098 showed the lowest binding energy also induced DNA damage in the Comet assay. CMK-0298 and CMK-0398 intercalated into DNA and induced mild DNA damage. All selected compounds, WWLL-013 in particular, were more cytotoxic toward the rat tumor cells than to the normal cells. In conclusion, the artemisinin derivatives such as CMK-0298, CMK-0398, WWLL-013, WWLL-022, and WWLL-1098 can be further developed as Topo 1 inhibitors.

Flavonolignans inhibit the arachidonic acid pathway in blood platelets

BACKGROUND

Arachidonic acid metabolism by cyclooxygenase (COX) is a major pathway for blood platelets' activation, which is associated with pro-thrombotic platelet activity and the production of pro-inflammatory mediators. Inhibition of COX activity is one of the major means of anti-platelet pharmacotherapy preventing arterial thrombosis and reducing the incidence of cardiovascular events. Recent studies have presented that a silymarin (standardized extract of Milk thistle (Silybum marianum)) can inhibit the COX pathway. Accordingly, the aim of our study was to determine the effects of three major flavonolignans (silybin, silychristin and silydianin) on COX pathway activity in blood platelets.

METHODS

We determined the effect of flavonolignans on arachidonic acid induced blood platelet aggregation, COX pathway metabolites formation, as well as COX activity in platelets. Additionally, we analysed the potential mechanism of this interaction using the bioinformatic ligand docking method.

RESULTS

We observed that tested compounds decrease the platelet aggregation level, both thromboxane A2 and malondialdehyde formation, as well as inhibit the COX activity. The strongest effect was observed for silychristin and silybin. In our in silico study we showed that silychristin and silybin have conformations which interact with the active COX site as competitive inhibitors, blocking the possibility of substrate binding.

CONCLUSIONS

The results obtained from this study clearly present the potential of flavonolignans as novel antiplatelet and anti-inflammatory agents.

Rational Drug Design Rational Drug Design

For the past three decades rationale drug design (RDD) has been developing as an innovative, rapid and successful way to discover new drug candidates. Many strategies have been followed and several targets with diverse structures and different biological roles have been investigated. Despite the variety of computational tools available, one can broadly divide them into two major classes that can be adopted either separately or in combination. The first class involves structure-based drug design, when the target's 3-dimensional structure is available or it can be computationally generated using homology modeling. On the other hand, when only a set of active molecules is available, and the structure of the target is unknown, ligand-based drug design tools are usually used. This review describes some recent advances in rational drug design, summarizes a number of their practical applications, and discusses both the advantages and shortcomings of the various techniques used.

The Comparison of Docking Search Algorithms and Scoring Functions

This chapter, composed of two parts, firstly provides molecular docking overview and secondly two molecular docking case studies are described. In overview, basic information about molecular docking are presented such as description of search algorithms and scoring functions applied in various docking programs. Brief description of methods utilized in some of the most popular docking programs also applied in our experimental work is provided. AutoDock, CDOCKER, GOLD, FlexX and FRED were used for docking studies of the DC-SIGN protein, while GOLD was further used for docking studies of cathepsin K protein. Methods and results of our studies with their contribution to science and medicine are presented. Content of the chapter is therefore appropriate for public of Medicinal and Organic Chemistry as an overview of docking studies, and also for Computational Chemists at the beginning of their work as the introduction to application of molecular docking programs.

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation

Membrane transporters mediate one of the most fundamental processes in biology. They are the main gatekeepers controlling active traffic of materials in a highly selective and regulated manner between different cellular compartments demarcated by biological membranes. At the heart of the mechanism of membrane transporters lie protein conformational changes of diverse forms and magnitudes, which closely mediate critical aspects of the transport process, most importantly the coordinated motions of remotely located gating elements and their tight coupling to chemical processes such as binding, unbinding and translocation of transported substrate and cotransported ions, ATP binding and hydrolysis, and other molecular events fueling uphill transport of the cargo. An increasing number of functional studies have established the active participation of lipids and other components of biological membranes in the function of transporters and other membrane proteins, often acting as major signaling and regulating elements. Understanding the mechanistic details of these molecular processes require methods that offer high spatial and temporal resolutions. Computational modeling and simulations technologies empowered by advanced sampling and free energy calculations have reached a sufficiently mature state to become an indispensable component of mechanistic studies of membrane transporters in their natural environment of the membrane. In this article, we provide an overview of a number of major computational protocols and techniques commonly used in membrane transporter modeling and simulation studies. The article also includes practical hints on effective use of these methods, critical perspectives on their strengths and weak points, and examples of their successful applications to membrane transporters, selected from the research performed in our own laboratory.

Molecular Characterization and Computational Modelling of New Delhi Metallo-β-Lactamase-5 from an Escherichia coli Isolate (KOEC3) of Bovine Origin

Emergence of antimicrobial resistance mediated through New Delhi metallo-β-lactamases (NDMs) is a serious therapeutic challenge. Till date, 16 different NDMs have been described. In this study, we report the molecular and structural characteristics of NDM-5 isolated from an Escherichia coli isolate (KOEC3) of bovine origin. Using PCR amplification, cloning and sequencing of full blaNDM gene, we identified the NDM type as NDM-5. Cloning of full gene in E. coli DH5α and subsequent assessment of antibiotic susceptibility of the transformed cells indicated possible role of native promoter in expression blaNDM-5. Translated amino acid sequence had two substitutions (Val88Leu and Met154Leu) compared to NDM-1. Theoretically deduced isoelectric pH of NDM-5 was 5.88 and instability index was 36.99, indicating a stable protein. From the amino acids sequence, a 3D model of the protein was computed. Analysis of the protein structure elucidated zinc coordination and also revealed a large binding cleft and flexible nature of the protein, which might be the reason for broad substrate range. Docking experiments revealed plausible binding poses for five carbapenem drugs in the vicinity of metal ions. In conclusion, results provided possible explanation for wide range of antibiotics catalyzed by NDM-5 and likely interaction modes with five carbapenem drugs.

Structural Insights into the Fluoroquinolone Resistance Mechanism of Shigella flexneri DNA Gyrase and Topoisomerase IV

Traveler's diarrhea (TD) is an important public health concern that can result from a variety of intestinal pathogens, including bacteria, parasites, and virus. A number of antibiotics are being used to cure TD, but due to widespread use of these antibiotics, the pathogens are becoming resistant to them. In this work, we performed docking studies of DNA gyraseA (GyrA) and topoisomerase IV (ParC) of Shigella flexneri and their mutants with two different fluoroquinolones, ciprofloxacin and norfloxacin, to understand their resistance mechanism at the structural level. S. flexneri strains with mutations at serine 83 to leucine and aspartic acid 87 to glutamate or asparagine of GyrA and that of serine 80 to isoleucine in ParC have decreased susceptibility to fluoroquinolones. This analysis revealed that interaction of ciprofloxacin/norfloxacin with all the mutants was weaker than the interaction of ciprofloxacin/norfloxacin with the wild type. This study highlights the importance of aspartic acid and serine in GyrA and that of serine in ParC, forming bonds with ciprofloxacin/norfloxacin, which may play a crucial role in antibiotic resistance. This work corelates very well with the experimental outcomes and gives a good explanation for fluoroquinolone resistance in S. flexneri.

Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids

Molecular docking of ligands to DNA-targets is of great importance for the design of new anticancer drugs. Unfortunately, most docking programs were developed for protein-ligand docking which raises a question about their applicability for the DNA-ligand docking. In this study, the popular docking programs AutoDock Vina, AutoDock4 and AutoDock3 were compared for a test set of 50 DNA-ligand complexes taken from the Nucleic Acid Database. It was shown that the version 3.05 of the AutoDock program was the most successful in reproducing the structures of intercalation and minor-groove complexes. The program AutoDock4 was able to re-dock to within 2 Å RMSD most of the intercalation complexes of the test set, but showed poor performance for minor groove binders. While Vina, on the contrary, failed to construct six intercalation complexes of the test set, but showed satisfactory results for DNA-ligand minor-groove complexes when small search space was used.

Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations

We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD) simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR) from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551). The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.

Polyphenol compounds belonging to flavonoids inhibit activity of coagulation factor X

Blood coagulation consists of series of zymogens which can be converted by limited proteolysis to active enzymes leading to the generation of thrombin and conversion of fibrinogen into fibrin by this enzyme. The activated factor X (FXa) forms prothrombinase complex on phosphatidylserine containing surface which is responsible for conversion of prothrombin to thrombin. One molecule of FXa generates more than 1000 thrombin molecules. Therefore FXa is a novel target for modern anticoagulant therapy. The aim of our present study is to examine the effects of the well-known plant polyphenolic compounds on factor Xa amidolytic activity and characterization of these interactions using bioinformatic ligand docking method. We observed that only four polyphenols belonging to flavonoids group: procyanidin B2, cyanidin, quercetin and silybin, had inhibitory effect on FXa activity. Bioinformatic analyses revealed that procyanidin B2, cyanidin, quercetin and silybin bound in the S1-S4 pockets located in vicinity of the FXa active site and blocked access of substrates to Ser195. The results presented here showed that flavonoids might be potential structural bases for design of new nature-based, safe, orally bioavailable direct FXa inhibitors.

Rational Drug Design

For the past three decades rationale drug design (RDD) has been developing as an innovative, rapid and successful way to discover new drug candidates. Many strategies have been followed and several targets with diverse structures and different biological roles have been investigated. Despite the variety of computational tools available, one can broadly divide them into two major classes that can be adopted either separately or in combination. The first class involves structure-based drug design, when the target's 3-dimensional structure is available or it can be computationally generated using homology modeling. On the other hand, when only a set of active molecules is available, and the structure of the target is unknown, ligand-based drug design tools are usually used. This review describes some recent advances in rational drug design, summarizes a number of their practical applications, and discusses both the advantages and shortcomings of the various techniques used.

Venus Flytrap (Dionaea muscipula Solander ex Ellis) Contains Powerful Compounds that Prevent and Cure Cancer

Chemoprevention uses natural or synthetic molecules without toxic effects to prevent and/or block emergence and development of diseases including cancer. Many of these natural molecules modulate mitogenic signals involved in cell survival, apoptosis, cell cycle regulation, angiogenesis, or on processes involved in the development of metastases occur naturally, especially in fruits and vegetables bur also in non-comestible plants. Carnivorous plants including the Venus flytrap (Dionaea muscipula Solander ex Ellis) are much less investigated, but appear to contain a wealth of potent bioactive secondary metabolites. Aim of this review is to give insight into molecular mechanisms triggered by compounds isolated from these interesting plants with either therapeutic or chemopreventive potential.

(1→3)-β-D-Glucan reduces the damages caused by reactive oxygen species induced in human platelets by lipopolysaccharides

LPS (lipopolysaccharide) induces platelet activation and is a well-known fundamental agent of septic shock and disseminated intravascular coagulation (DIC). Biological activity of (1→3)-β-D-glucan is related due to its anti-inflammatory, antioxidant, and antitumor properties. We focus our attention on the (1→3)-β-D-glucan (antiplatelet) properties. The main purpose of our study was to evaluate the influence of (1→3)-β-D-glucan from Saccharomyces cerevisiae on destructive activity of LPS (from Escherichia coli and Pseudomonas aeruginosa) on human blood platelets. We assess biochemically in vitro if (1→3)-β-D-glucan might combat the oxidative stress caused by LPS stroke associated with nitrative and oxidative damages of human platelet biomolecules. We also make an attempt by in silico molecular docking to determine the interactions between the molecules of (1→3)-β-D-glucan and LPS. Our conclusion is that protective mechanism of (1→3)-β-D-glucan against LPS action on blood platelets is due to as well: its antioxidant properties, as to its interaction with LPS-binding region of TLR4-MD-2 complex.

Visualizing functional motions of membrane transporters with molecular dynamics simulations

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.