Current Drug Discovery Technologies (v.14, #3)

Meet Our Regional Editor by Yiyun Cheng (141-141).

PBPK Modeling - A Predictive, Eco-Friendly, Bio-Waiver Tool for Drug Research by Baishakhi De, Koushik Bhandari, Ranjan Mukherjee, Prakash Katakam, Shanta K. Adiki, Rohit Gundamaraju, Analava Mitra (142-155).
Background: The world has witnessed growing complexities in disease scenario influenced by the drastic changes in host-pathogen- environment triadic relation. Pharmaceutical R&Ds are in constant search of novel therapeutic entities to hasten transition of drug molecules from lab bench to patient bedside. Extensive animal studies and human pharmacokinetics are still the “gold standard” in investigational new drug research and bio-equivalency studies. Apart from cost, time and ethical issues on animal experimentation, burning questions arise relating to ecological disturbances, environmental hazards and biodiversity issues. Grave concerns arises when the adverse outcomes of continued studies on one particular disease on environment gives rise to several other pathogenic agents finally complicating the total scenario. Thus Pharma R&Ds face a challenge to develop bio-waiver protocols. Lead optimization, drug candidate selection with favorable pharmacokinetics and pharmacodynamics, toxicity assessment are vital steps in drug development.

Methods: Simulation tools like Gastro Plus, PK Sim®, SimCyp find applications for the purpose. Advanced technologies like organ-on-a chip or human-on-a chip where a 3D representation of human organs and systems can mimic the related processes and activities, thereby linking them to major features of human biology can be successfully incorporated in the drug development tool box.

Results: PBPK provides the State of Art to serve as an optional of animal experimentation. PBPK models can successfully bypass bio-equivalency studies, predict bioavailability, drug interactions and on hyphenation with in vitro-in vivo correlation can be extrapolated to humans thus serving as bio-waiver.

Conclusion: PBPK can serve as an eco-friendly bio-waiver predictive tool in drug development.

Background: Pseudomonas aeruginosa is an opportunistic pathogen problematic in causing nosocomial infections and is highly susceptible to development of resistance to multiple antibiotics. The gene encoding methionyl-tRNA synthetase (MetRS) from P. aeruginosa was cloned and the resulting protein characterized.

Methods: MetRS was kinetically evaluated and the KM for its three substrates, methionine, ATP and tRNAMet were determined to be 35, 515, and 29 ?M, respectively. P. aeruginosaMetRS was used to screen two chemical compound libraries containing 1690 individual compounds.

Results: A natural product compound (BM01C11) was identified that inhibited the aminoacylation function. The compound inhibited P. aeruginosa MetRS with an IC50 of 70 ?M. The minimum inhibitory concentration (MIC) of BM01C11 was determined against nine clinically relevant bacterial strains, including efflux pump mutants and hypersensitive strains of P. aeruginosa and E. coli. The MIC against the hypersensitive strain of P. aeruginosa was 16 ?g/ml. However, the compound was not effective against the wild-type and efflux pump mutant strains, indicating that efflux may not be responsible for the lack of activity against the wild-type strains. When tested in human cell cultures, the cytotoxicity concentration (CC50) was observed to be 30 ?g/ml. The compound did not compete with methionine or ATP for binding MetRS, indicating that the mechanism of action of the compound likely occurs outside the active site of aminoacylation.

Conclusion: An inhibitor of P. aeruginosa MetRS, BM01C11, was identified as a flavonoid compound named isopomiferin. Isopomiferin inhibited the enzymatic activity of MetRS and displayed broad spectrum antibacterial activity. These studies indicate that isopomiferin may be amenable to development as a therapeutic for bacterial infections.

Molecularly Imprinted Polymer of Colocynthin, An Effective Tool for Quality Control of Citrullus colocynthis Extracts by Ramezani Farid, Khanavi Mahnaz, Shams Ardekani Mohammad Reza, Sellergren Börje, Eftekhari Mahdieh, Rastegar Hossein, Shekarchi Maryam (169-180).
Background: Different parts of Colocynth, Citrullus colocynthis (L.) Schrad., are used in traditional phytotherapy and homeopathy.

Objective: In our new approach, a molecularly imprinted polymer was synthesized to absorb colocynthin, the major plant marker, and its capability was evaluated using HPLC-UV.

Method: A new method was considered to achieve optimal conditions. FT-infrared, N2 adsorption porosimetry, fluorescent and scanning electron microscopy and thermo gravimetric profile of the polymers were studied. The imprinted polymer was applied as molecularly imprinted solid phase extraction sorbent to enrich colocynthin from colocynth oil extract, a traditional medicine dosage form.

Results: The imprinted polymer showed high capacity and affinity toward colocynthin. Physical assessments demonstrated no major differences between imprinted and nonimprinted polymers. The imprinted polymer was able to absorb colocynthin more efficiently than non-imprinted and control simple solvent extraction from the real sample.

Conclusion: In conclusion, this polymer is capable of being applied as a promising adsorbent for analysis of colocynth traditional medicine products.

Grid-based Continual Analysis of Molecular Interior for Drug Discovery, QSAR and QSPR by Andrey V. Potemkin, Maria A. Grishina, Vladimir A. Potemkin (181-205).
Background: In 1979, R.D.Cramer and M.Milne made a first realization of 3D comparison of molecules by aligning them in space and by mapping their molecular fields to a 3D grid. Further, this approach was developed as the DYLOMMS (Dynamic Lattice- Oriented Molecular Modelling System) approach. In 1984, H.Wold and S.Wold proposed the use of partial least squares (PLS) analysis, instead of principal component analysis, to correlate the field values with biological activities. Then, in 1988, the method which was called CoMFA (Comparative Molecular Field Analysis) was introduced and the appropriate software became commercially available. Since 1988, a lot of 3D QSAR methods, algorithms and their modifications are introduced for solving of virtual drug discovery problems (e.g., CoMSIA, CoMMA, HINT, HASL, GOLPE, GRID, PARM, Raptor, BiS, CiS, ConGO,). All the methods can be divided into two groups (classes):1. Methods studying the exterior of molecules; 2) Methods studying the interior of molecules.

Methods: A series of grid-based computational technologies for Continual Molecular Interior analysis (CoMIn) are invented in the current paper. The grid-based analysis is fulfilled by means of a lattice construction analogously to many other grid-based methods. The further continual elucidation of molecular structure is performed in various ways. (i) In terms of intermolecular interactions potentials. This can be represented as a superposition of Coulomb, Van der Waals interactions and hydrogen bonds. All the potentials are well known continual functions and their values can be determined in all lattice points for a molecule. (ii) In the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum free-orbital approach AlteQ is proposed. All the functions can be calculated using a quantum approach at a sufficient level of theory and their values can be determined in all lattice points for a molecule. Then, the molecules of a dataset can be superimposed in the lattice for the maximal coincidence (or minimal deviations) of the potentials (i) or the quantum functions (ii).

Results: The methods and criteria of the superimposition are discussed. After that a functional relationship between biological activity or property and characteristics of potentials (i) or functions (ii) is created. The methods of the quantitative relationship construction are discussed. New approaches for rational virtual drug design based on the intermolecular potentials and quantum functions are invented. All the invented methods are realized at www.chemosophia.com web page.

Conclusion: Therefore, a set of 3D QSAR approaches for continual molecular interior study giving a lot of opportunities for virtual drug discovery, virtual screening and ligand-based drug design are invented. The continual elucidation of molecular structure is performed in the terms of intermolecular interactions potentials and in the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum free-orbital approach AlteQ is proposed. The methods of the quantitative relationship construction are discussed. New approaches for rational virtual drug design based on the intermolecular potentials and quantum functions are invented. All the invented methods are realized at www.chemosophia.com web page.

The Potent Inhibitory Effect of ?-D-Mannuronic Acid (M2000) as a Novel NSAID with Immunosuppressive Property on Anti-Cyclic Citrullinated Peptide Antibodies, Rheumatoid Factor and Anti-dsDNA Antibodies in Patients with Rheumatoid Arthritis by Hossein Ahmadi, Ahmad R. Jamshidi, Mahdi Mahmoudi, Salvatore Cuzzocrea, Mohammad Javad Fattahi, Anis Barati, Bernd H. A. Rehm, Hidenori Matsuo, Abbas Mirshafiey (206-214).
Objective: To investigate the inhibitory effect of ?-D-mannuronic acid (M2000) on anti-cyclic citrullinated peptide antibodies (anti-CCP), rheumatoid factor (RF), antidouble strand DNA (anti-dsDNA) and acute phase reactants in rheumatoid arthritis (RA) patients.

Methods: The study included 40 patients with RA who had an inadequate response to conventional therapy (identifier: IRCT2014011213739N2). The patients were permitted to continue the conventional therapy excluding NSAIDs. 21 of them were treated orally by M2000 at a dose of 500 mg twice daily for 12 weeks and the others did not. Serum samples were collected at baseline, 4 weeks and 12 weeks after treatment and were tested for the serum level of anti-CCP and anti-dsDNA antibodies using enzyme linked immunosorbent assay. The serum level of RF and C-reactive proteins (CRP) was determined by the immunoturbidimetric assay, respectively.

Results: At baseline, all patients in the M2000 treated group and the control group were positive for anti-CCP, RF. moreover, 4 of 21 (19%) in the M2000 treated group and 2 of the 19 (10.5%) patients in the control group were positive for anti-dsDNA antibodies, respectively. The serum levels of anti-CCP, RF and anti-dsDNA were decreased significantly after M2000 therapy (p<0.001, p<0.001 and p<0.001, respectively). The reduction in the level of anti-CCP was positively correlated with disease activity, swollen joint count and CRP. Furthermore, the level of inflammatory markers ESR and CRP decreased significantly after M2000 therapy (p<0.001 and p<0.004, respectively).

Conclusion: M2000 shows inhibitory effect on anti-CCP, RF, anti-dsDNA antibodies and acute phase reactants in RA patients.