Shunsuke Aoki

PLGA artificial nerve conduits with dental pulp cells promote facial nerve regeneration

A number of recent studies have shown the effectiveness of tubulation, using neural progenitor cells or Schwann cells, for promoting nerve regeneration. However, the use of neural cells from other neural donor tissues has potentially serious clinical complications. Therefore, we focused on dental pulp as a new cell source for use in such artificial conditions. Previously, we showed that silicone tubes filled with dental pulp cells (DPCs) promoted facial nerve regeneration in rats. However, the use of silicone tubes requires a secondary removal operation because they may give rise to chronic inflammation and pain. Therefore, to avoid this procedure, a new artificial device was prepared from a degradable poly‐DL‐lactide‐co‐glycolide (PLGA) tube containing DPCs, and its effectiveness for repairing gaps in the facial nerves of rats was investigated. A PLGA tube containing rat DPCs embedded in a collagen gel was transplanted into a gap in a rat facial nerve. Five days after transplantation, the facial nerves connected by the PLGA tubes containing DPCs were repaired more quickly than the control nerves. The PLGA tubes were resorbed in vivo and nerve regeneration was observed 2 months after the transplantation. Immunostaining showed that Tuj1‐positive axons were present in the regenerated nerves 2 months after transplantation, and osmium–toluidine blue staining showed no mineralization of the regenerated nerves in those tubes containing myelinated fibres after 9 weeks. PLGA tubes filled with DPCs promoted nerve regeneration and were readily resorbed in vivo. Copyright

Hepatocyte growth factor and Met in drug discovery

Activation of the hepatocyte growth factor (HGF)-Met pathway evokes dynamic biological responses that support the morphogenesis, regeneration and survival of cells and tissues. A characterization of conditional Met knockout mice indicates that the HGF-Met pathway plays important roles in the regeneration, protection and homeostasis of cells such as hepatocytes, renal tubular cells and neurons. Preclinical studies in disease models have indicated that recombinant HGF protein and expression plasmid for HGF are biological drug candidates for the treatment of patients with diseases or injuries that involve impaired tissue function. The phase-I and phase-I/II clinical trials of the intrathecal administration of HGF protein for the treatment of patients with amyotrophic lateral sclerosis and spinal cord injury, respectively, are ongoing. Biological actions of HGF that promote the dynamic movement, morphogenesis and survival of cells also closely participate in invasion-metastasis and resistance to the molecular-targeted drugs in tumour cells. Different types of HGF-Met pathway inhibitors are now in clinical trials for treatment of malignant tumours. Basic research on HGF and Met has lead to drug discoveries in regenerative medicine and tumour biology.

Identification of novel potential antibiotics for tuberculosis by in silico structure-based drug screening

The enoyl-acyl carrier protein reductase of Mycobacterium tuberculosis (MTB) is a key enzyme of the type II fatty acid synthesis system. It is involved in the production of mycolic acid and is a known target for isoniazid, an effective antibiotic for tuberculosis treatment. The increasing prevalence of tuberculosis in many areas of the world, which is associated with the rise of drug-resistant MTB strains, presents a major global health threat. In this study, we attempted to identify novel antibiotics specifically targeting the MTB enoyl-acyl carrier protein reductase. We performed in silico structure-based drug screening using the crystal structure data for the MTB enoyl-acyl carrier protein reductase (PDB code; 2H7I) and a virtual compound library, which includes 152,102 chemicals. By a two-step screening method using DOCK (first screening) and GOLD (second screening), we identified 5 chemical compounds expected to have high binding affinity to the active center of the MTB enoyl-acyl carrier protein reductase. Moreover, we examined the antibiotic effects of these chemical compounds on model bacterial strains by in vitro experiments. We found that a chemical compound, which has a basic skeleton comprised of dibenzofuran, acetoamide, trizol, furyl and methylphenyl groups, completely inhibited the growth of Mycobacterium vanbaalenii and had no toxic effects on enterobacteria and cultured mammalian cells. Therefore, the chemical compound is likely to be useful in the research and development of new antibiotics for tuberculosis.

Surgical anatomy of the swine face

In order to develop tissue engineering applications for oral and maxillofacial surgery, the surgical anatomy of the miniature pigs face was investigated in three miniature pig cadavers and three anaesthetized miniature pigs using identical procedures that were previously described for humans. A preauricular incision with a retromandibular and a submandibular extension was initially made through the facial skin and subcutaneous tissues. The underlying tissues were then carefully dissected in order to progressively expose the platysma muscle, the superficial layer of deep cervical fascia, the marginal mandibular branch and buccal branch of the facial nerve, the mental nerve and the mandibular skeleton. The marginal mandibular branch of the facial nerve has an upper and lower division. Stimulation of the facial nerve and its branches showed that the upper division of the marginal mandibular branch innervates muscles and tissues in the upper lip and nose region, and the lower division innervates muscles and tissues in the lower lip region. The gross anatomy of the maxillofacial region in the pigs was found to be similar to that of humans. Although the distributions of the marginal mandibular branch of the facial nerve and the mental nerve are different from that of humans, we concluded that miniature pigs are a suitable experimental model for the preclinical development of tissue engineering applications in oral and maxillofacial surgery.

Identification of Compounds with Potential Antibacterial Activity against Mycobacterium through Structure-Based Drug Screening

To identify novel antibiotics against Mycobacterium tuberculosis, we performed a hierarchical structure-based drug screening (SBDS) targeting the enoyl-acyl carrier protein reductase (InhA) with a compound library of 154,118 chemicals. We then evaluated whether the candidate hit compounds exhibited inhibitory effects on the growth of two model mycobacterial strains: Mycobacterium smegmatis and Mycobacterium vanbaalenii. Two compounds (KE3 and KE4) showed potent inhibitory effects against both model mycobacterial strains. In addition, we rescreened KE4 analogs, which were identified from a compound library of 461,383 chemicals through fingerprint analysis and genetic algorithm-based docking simulations. All of the KE4 analogs (KES1-KES5) exhibited inhibitory effects on the growth of M. smegmatis and/or M. vanbaalenii. Based on the predicted binding modes, we probed the structure-activity relationships of KE4 and its analogs and found a correlative relationship between the IC50 values and the interaction residues/LogP values. The most potent inhibitor, compound KES4, strongly and stably inhibited the long-term growth of the model bacteria and showed higher inhibitory effects (IC50 = 4.8 μM) than isoniazid (IC50 = 5.4 μM), which is a first-line drug for tuberculosis therapy. Moreover, compound KES4 did not exhibit any toxic effects that impede cell growth in several mammalian cell lines and enterobacteria. The structural and experimental information of these novel chemical compounds will likely be useful for the development of new anti-TB drugs. Furthermore, the methodology that was used for the identification of the effective chemical compound is also likely to be effective in the SBDS of other candidate medicinal drugs.

Discovery of InhA inhibitors with anti-mycobacterial activity through a matched molecular pair approach.

The Mycobacterium tuberculosis (M. tuberculosis) enoyl-acyl carrier protein reductase (mtInhA) is an attractive enzyme and a thoroughly studied target for tuberculosis therapy. In this study, to identify novel structure-activity relationships (SARs) of mtInhA inhibitors, a series of diphenyl ether derivatives were designed based on the matched molecular pair (MMP) method, and the binding energies of these compounds were subsequently estimated by in silico structure-based drug screening (SBDS) to provide more useful data. Consequently, the 10 unique candidate compounds (KEM1-KEM10) were identified and assessed for the inhibition of mtInhA enzymatic activity, in vitro antibiotic effects against model mycobacteria and toxicity level on both intestinal bacteria and mammalian cells. Among the compounds tested, phenyl group (KEM4) and 2-fluorobenzyl group (KEM7) substitutions produced preferable inhibitory effects on mtInhA enzymatic activity relative to those provided by a furyl group (KES4: base compound) at the terminal of the compound, and KEM7 inhibited the growth of the mycobacteria strain with a lower IC50 value. Moreover, most of the candidate compounds exhibited neither inhibition of the growth of enterobacteria nor toxic effects on mammalian cells, though KEM10 exhibited toxicity against cultured MDCK cells. The structural and experimental information concerning these mtInhA inhibitors identified through MMP-based in silico screening will likely contribute to the lead optimisation of novel antibiotics for M. tuberculosis.

Identification of novel antimycobacterial chemical agents through the in silico multi-conformational structure-based drug screening of a large-scale chemical library.

The increasing prevalence of drug-resistant tuberculosis, which is resistant to effective multiple antibiotic, presents a major global health threat. The thymidine monophosphate kinase (TMPK) of Mycobacterium tuberculosis (M.xa0tuberculosis), which is an essential enzyme for the maintenance of the thymidine triphosphate pools, is considered an attractive target for the development of effective antibiotics against tuberculosis. In this study, we attempted to identify novel chemical compounds that specifically target the M.xa0tuberculosis TMPK (mtTMPK). We performed in silico structure-based drug screening using the crystal structure data of mtTMPK and a large-scale virtual compound library, which is composed of 6,192,930 chemicals. Through a three-step screening method using the DOCK and GOLD, we identified ten chemical compounds that were predicted to have high binding affinity to the active site cleft of the mtTMPK. We then evaluated the antibiotic effects of these chemical compounds on model mycobacteria strains. As a result, we found that a chemical compound, K10, completely inhibited the growth of Mycobacterium vanbaalenii (M.xa0vanbaalenii) and Mycobacterium smegmatis (M.xa0smegmatis). Moreover, K10 does not exhibit any toxic effects on the growth of enterobacteria and mammalian cells. The structural and experimental information regarding this novel chemical compound, K10, is likely to be useful for the hit-to-lead optimization of new antibiotics for the treatment of tuberculosis.

Identification of novel potential antibiotics against Staphylococcus using structure-based drug screening targeting dihydrofolate reductase.

The emergence of multidrug-resistant Staphylococcus aureus (S. aureus) makes the treatment of infectious diseases in hospitals more difficult and increases the mortality of the patients. In this study, we attempted to identify novel potent antibiotic candidate compounds against S. aureus dihydrofolate reductase (saDHFR). We performed three-step in silico structure-based drug screening (SBDS) based on the crystal structure of saDHFR using a 154,118 chemical compound library. We subsequently evaluated whether candidate chemical compounds exhibited inhibitory effects on the growth of the model bacterium: Staphylococcus epidermidis (S. epidermidis). The compound KB1 showed a strong inhibitory effect on the growth of S. epidermidis. Moreover, we rescreened chemical structures similar to KB1 from a 461,397 chemical compound library. Three of the four KB1 analogs (KBS1, KBS3, and KBS4) showed inhibitory effects on the growth of S. epidermidis and enzyme inhibitory effects on saDHFR. We performed structure–activity relationship (SAR) analysis of active chemical compounds and observed a correlative relationship among the IC50 values, interaction residues, and structure scaffolds. In addition, the active chemical compounds (KB1, KBS3, and KBS4) had no inhibitory effects on the growth of model enterobacteria (E. coli BL21 and JM109 strains) and no toxic effects on cultured mammalian cells (MDCK cells). Results obtained from Protein Ligand Interaction Fingerprint (PLIF) and Ligand Interaction (LI) analyses suggested that all of the active compounds exhibited potential inhibitory effects on mutated saDHFR of the drug-resistant strains. The structural and experimental information concerning these novel chemical compounds will likely contribute to the development of new antibiotics for both wild-type and drug-resistant S. aureus.

Computational Medicinal Chemistry for Rational Drug Design: Identification of Novel Chemical Structures with Potential Anti-Tuberculosis Activity

Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis and is a common infectious disease with high mortality and morbidity. The increasing prevalence of drug-resistant strains of TB presents a major public health problem. Due to the lack of effective drugs to treat these drug-resistant strains, the discovery or development of novel anti-TB drugs is important. Computer-aided drug design has become an established strategy for the identification of novel active chemicals through a combination of several drug design tools. In this review, we summarise the current chemotherapy for TB, describe attractive target proteins for the development of antibiotics against TB, and detail several computational drug design strategies that may contribute to the further identification of active chemicals for the treatment of not only TB but also other diseases.

A protocol for immunofluorescence staining of floating neurospheres

This protocol describes the immunofluorescence staining of floating neurospheres in culture plates. Although this protocol is similar to conventional immunofluorescence staining, the staining procedure of floating neurospheres in multiwell culture plates and the washing procedure are different. Neurospheres in culture plates are transferred to a 12-well plate using a 200-1000microL pipette. The spheres are precipitated by gravity for 3min. Then, the 12-well plate is tilted slightly, and the culture medium is aspirated by the pipette. After aspiration, the spheres are visually verified to be at the bottom of the wells. PBS (400microL) is added to the well for washing the spheres. This procedure is repeated three times. This protocol is easier than a conventional procedure using cryostat sections and can give clear sphere structures.