Interaction of some bacterial proteins with ligands using molecular docking.
Abstract
Drug delivery system (DDS) is an important challenge in medicine over the conventional drug delivery system in case of therapeutic efficacy. In recent years, due to the shortcomings of conventional chemotherapy such as poor bioavailability, low treatment index, and unclear side effects, the focus of drug development and research has shifted to new nanocarriers of chemotherapeutic drugs. By using biodegradable materials, nanocarriers generally have the advantages of good biocompatibility, low side effects, specific target, controlled release profile, and improved efficacy. There are many kinds of DDS such as lyposome, vesicle, peptide, gene, microchip, polysaccharide and so on being studied nowadays. Each DDS has the advantages and disadvantage. However, the materials made them are expensive and the preparation techniques sometimes are complicated. Moreover, those DDS are rarely shown the ability in drug delivery to target. In the study, nano sized bacterial minicells were showed to clarify the importance of this material in drug delivery and target therapy.
Keywords
- bacteria
- minicells
- interaction of minicell components and drugs
- molecular docking
- drug delivery systems
- nanoparticles
1. Introduction
The drug is delivered via entering the body, traveling through the bloodstream to go to the target and then eliminating out of the body [1, 2]. DDS is oriented to limit unwanted effects in human pharmacology. DDS must be biodegradable in the body, suggesting that DDS should be researched and exploited from various materials to obtain high bioavailability toward the target from which the possibility of drug resistance and side effects will be reduced, in addition to carrying drugs. Lyposomes, peptides, vesicles, polysaccharides, aptamers, viruses, and DNA are much being researched. However, each DDS can bring drugs and especially toward the target is valuable. Furthermore, targeted DDS is developed to achieve a higher level of treatment due to the disease target specificity but reduce side effects. Nanoparticles can also accumulate in the healthy organ where they can cause side effects [3, 4]. Nanoparticles must be potential to the target of the body, control drug release, and dramatically increase the bioavailability of active compounds. Various materials have been used to prepare nanoparticles for drug delivery systems. Liposome, polymer and minicell conjugated drugs were taken the preclinical trials. The first biodegradable nanoparticles are developed for drug delivery with the properties of lipid membranes such as Doxil [5]. According to the US National Cancer Institute, nanoparticles are currently authorized for use in the global market, while the cost of these products is ten times higher than conventional treatments [6]. At present, the use of nano-sized particles derived from bacteria which are called minicells to encapsulate a wide range of different chemotherapeutic drugs is a new technology that specifically targets to receptors on disease cell surface via dual-specific antibodies coated on the minicells. Minicell loaders have been shown the apoptosis effects on tumor cells both
2. Well-known drug delivery systems
2.1 Advantages of well-known DDSs
There are many drugs that are effective for treating diseases, but side-effects are still problematic when crossing the barriers in the body, for example eye barrier, colon, and brain membrane due to the complex structure of barriers of eye, colon, and brain. DDS can be microelectromechanical (MEM)-based device, polymer matrix or gene delivery system. DDS can be developed using pH, enzyme, time, pressure-controlled delivery method [9]. In some cases of colon treatment, a hole in the membrane is covered by an enteric-coated polymer to prevent drug release in the upper gastrointestinal tract. Brain-targeted drug delivery has received increasing attention over the past decade. Many strategies have been developed to improve brain-targeted drug delivery by fabricating particle-based drug delivery systems. Despite impressive progress, drug delivery efficiency remains unsatisfactory. Recent advances in the field of microfabrication have made possible the development of controlled release systems for drug delivery. Drug delivery has achieved tremendous development over the past two decades, but regulating drug delivery to the brain is going on a daunting task. By using such highly specialized transport mechanisms, it is possible to efficiently mediate the penetration of the nanodrug delivery system into the brain. Surface functionalization of DDS and selection of suitable materials for their membranes play an important role in drug release kinetics. The release of a particular drug from DDS can be regulated by external or internal stimuli. The pH-responsive DDS can only release the drug in the area it targets. Several pH-responsive DDSs have been successfully engineered to deliver drugs in tumor tissues because tumor tissues have a different pH than healthy tissues [10]. The reduced environment of the cytoplasmic fluid of the cell relative to the body fluid becomes a stimulus for redox-sensitive DDS to release active substances only in the cytosol but not in the body fluid [11]. Magnetic NPs loaded with therapeutic agents can be guided, using an externally applied magnetic field, to a specific organ and stimulated to release the drug only at that location [12]. Nanotechnology was first defined in 1974 by Norio Taniguchi of Tokyo University of Science, as the technique and technology for understanding and controlling matter at the length scale of about 1 to 100 nanometers [1]. Many nanomaterial preparations have significant potential applications for therapeutic drug delivery systems. Several nano-sized preparations such as liposomes, polymeric micelles and polymer drug conjugates have been developed
2.2 Challenges of well-known DDSs
Undoubtedly, the controlled DDS presents an important challenge in medicine when compared with the conventional DDS in the case of therapeutic efficacy. Accordingly, there has been a search for drug delivery systems that enhanced activity for more drugs with fewer complications. Until now, there are very few reports on the effects of nanoparticles on the body. The long-term effects on our health are difficult to predict and understand. Nanocarriers can increase the stability of many anticancer drugs by integrating them into their structures, for example, the stability of doxorubicin has also been increased through its incorporation into liposomes [20]. Previous reports showed a beneficial effect on the long-term stability of DNA when the molecule was complexed into polymeric micelles [21, 22]. Furthermore, the nanoparticles are antibacterial agents but can also kill the good bacteria in the gut. In addition, DDSs using nanoparticles are more expensive to manufacture than traditional materials because of the many complex steps [18]. Consequently, it is difficult to scale up the production of nanoparticles leading to the limited production in the market and also causing to many risks due to their unknown side effects. Drug delivery using nanoparticles is increasingly popular and faces many challenges in pharmaceutical engineering. There are many reports on nanotoxicology, the potential negative effects of interactions between nanomaterials and biological systems. For example, naked quantum dots exhibit cytotoxicity by generating reactive oxygen species, leading to nuclear, mitochondrial, and plasma membrane damage [17]. For silica nanoparticles, concentrations above 0.1 mg/ml were found to be toxic, as demonstrated by decreased cell proliferation and availability [17]. The production of carbon nanotubes also induced the formation of reactive oxygen species, mitochondria dysfunction, lipid peroxidation, and changes in cell morphology. In addition, it has been reported that most cationic NPs can induce hemolysis and coagulation, while neutral and anionic NPs did not show toxicity [23, 24]. For hydrophobic drugs, their main limitation is their low solubility at the absorption site and poor biodegradability. The case of many common hydrophobic drugs is well illustrated by paclitaxel that have low oral bioavailability in conventional formulations but the activity increase when formulated in DDS like liposome [25, 26, 27]. However, DDS which can carry different kinds of drugs to the disease target are challenged. Therefore, finding out the potential DDS is essential. In this chapter, bacterial minicells that have nano size are focused to show its ability in drug delivery.
3. Minicells in drug delivery
3.1 Minicells generated by microorganisms
Minicells are the small cells in nano size that can be call nanoparticles. They are made from the membranes of mutant bacteria during cell division cycle. The term “minicells” refers to cells that contain RNA and proteins but only small amounts of chromosomal DNA, if any at all. The genetic and biochemical characterization of the minicells of
3.2 Minicell loading with different drugs
Interestingly, minicells can be packed with 1–10 million drug molecules [17]. Minicells traverse tumor cells by receptor-mediated endocytosis.
By molecular docking application, different kinds of proteins of bacteria are expected to interact with a variety of ligands such as drugs. Molecular docking is a method to predict the drug molecule which can be bind to the proteins of the disease target based on a computation aid. In this study, protein-ligand concatenation was performed to see the ability of drugs in interacting with the target protein [42]. The 3D crystal structures of proteins from bacteria was obtained from the Protein Data Bank (PDB). Moreover, all the 3D structures of ligands like drugs were downloaded in Pubchem and ChemSpider [43]. Then, Autodock Vina were used to screen protein and ligand interaction, providing the binding affinity of each profile between the ligand and protein interactions. The Genetic Algorithm was calculated based on 10 runs for 10 different configurations of drugs to show the binding ability to the target protein [43]. Validation is based on Root Mean Standard Deviation (RMSD) value and the binding energy value (Kcal/mol) [44]. Interactions with amino acid residues in the receptor’s active binding pocket were analyzed using BIOVIA Discovery Studio binding [45, 46]. The interactions between some proteins of
Number | Proteins | Ligands | Binding energy (kcal/mol) |
---|---|---|---|
1 | Maltose-bound maltose sensor engineered by insertion of circularly permuted green fluorescent protein into | Vancomycin | −23.4 |
Vincristine | −20.7 | ||
Paclitaxel | −19.8 | ||
Stigmasterol | −9.9 | ||
Quercetin | −8.6 | ||
Cephalexin | −7.7 | ||
Ciprofloxacin | −7.7 | ||
Erythromycin | −7.6 | ||
Penicillin | −7.6 | ||
Hydroxychloroquine | −7.4 | ||
2 | The 2.4A crystal structure of OmpA domain of OmpA from | Vancomycin | −19.1 |
Vincristine | −17 | ||
Vinblastine | −16.8 | ||
Paclitaxel | −15.9 | ||
Quercetin | −8 | ||
Stigmasterol | −7.3 | ||
Penicillin | −7 | ||
Ciprofloxacin | −7 | ||
Erythromycin | −6.9 | ||
Cephalexin | −6.8 | ||
Hydroxychloroquine | −5.9 | ||
3 | The host outer membrane proteins OmpA and OmpC are packed at specific sites in the | Vancomycin | −21.6 |
Vincristine | −17.3 | ||
Vinblastine | −16.8 | ||
Paclitaxel | −16.8 | ||
Stigmasterol | −7.9 | ||
Quercetin | −7.8 | ||
Hydroxychloroquine | −5.7 | ||
Erythromycin | −8.2 | ||
Penicillin | −7 | ||
Cephalexin | −7.3 | ||
Ciprofloxacin | −7 | ||
4 | The structure of the dimeric | Paclitaxel | −19.7 |
Vancomycin | −17.8 | ||
Vinblastine | −14.7 | ||
Vincristine | −14.6 | ||
Erythromycin | −11.5 | ||
Stigmasterol | −7.0 | ||
Ciprofloxacin | −6.3 | ||
Cephalexin | −6.2 | ||
Quercetin | −6.1 | ||
Penicillin | −5.7 | ||
Hydroxychloroquine | −5.0 | ||
5 | Solution structure of | Vancomycin | −17.5 |
Vincristine | −16.9 | ||
Vinblastine | −15.9 | ||
Paclitaxel | −13.1 | ||
Erythromycin | −13.0 | ||
Quercetin | −7.4 | ||
Stigmasterol | −6.5 | ||
Ciprofloxacin | −5.7 | ||
Cephalexin | −5.3 | ||
Penicillin | −5 | ||
Hydroxychloroquine | −4.8 |
As seeing in Table 1, beside outer membrane proteins could bind to drugs, cell division protein inhibitors such as MinC and MinD could interact to different drugs. Figure 2 showed the representative studies of molecular docking for screening the interaction of MinD cell division inhibitor of
4. Conclusion
Nowadays, DDS is developed for targeting to therapy. With the small size like nanoparticle, the bioavailability of drugs increases. However, nanotechnology is still challenged. Some materials are not convenient for DDS development. Moreover, DDS which carries drug to the target to reduce side effect is very important for human health care. Bacterial minicells are cheap and can be produced in large scale. With the complexity of cell wall structure, minicells can bind with hydrophobic and hydrophilic drugs. Especially, minicells could bind to monoclonal antibodies which are specific to the target cells. Exploiting minicells give a good picture for cancer therapy, pathogen treatment and vaccine development.
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