SCHIZOPHRENIA: A LOOK FORWARD WITH ZINC06025953

SCHIZOPHRENIA: A LOOK FORWARD WITH ZINC06025953

Rituraj ^* and K. K. Srivastava

Department of Chemistry, Vinoba Bhave University, Hazaribag, Jharkhand, India.

ABSTRACT: Phosphodiesterase PDE10A is an enzyme that has established connection earlier with schizophrenic condition, schizophrenia is well known severely chronic and disabling disease worldwide today. Unfortunately, there is no concrete evidence till day to point out as a single cause of this disease. However, in a recent work a research team of Merck Research Group recognized earlier pyp-1 as an effective drug like lead(DLL) after a long term “in vitro” experimentations, to inhibit phosphodiesterase PDE10A to control the schizophrenic conditions. Herein we carry forward this work to “in silico” way to find similar/more efficient molecules in “ZINC” DL (Drug Like) molecular structure bank (zincdocking.org) in consideration with pyp-1 as a standard molecular structure for our work, docking has been performed with separated DL (Drug Like) molecular structures as similar to “pyp-1”, using similarity measures “tanimoto” binding efficacy and drug properties are computed out and analyzed, the outcomes of that work has been reported.  The ZINC06025953 molecular structure pointed out that it may acts as a potential drug like lead(DLL), it all on that of the computation ground. Further, need the herein virtual laboratory work an experimental verification, for that synthesis and drug ability check out, off course in a real laboratory equipped with adequate facilities.

Phosphodiesterase, PDE10A, pyp-1, Schizophrenia, ZINC06025953

INTRODUCTION: Psychiatric disorders such as depression, anxiety and a severely major one schizophrenia are leading causes of disability in humans, on another hand Pathogenesis of psychiatric disorders remain challenging and elusive, drug discovery is still ambiguous and very complicated till day along the globe. In 1999, phosphodiesterase (PDE10A) is identified as a promising target for the treatment of schizophrenia ¹, it well established earlier that it intervene in the various cellular responses that regulated by the second messengers like cAMP and cGMP in the medium spiny neurons of the mammalian striatum,

which involved in cognitive function in coordination to the proper body movement and individual motivation. Striatum (part of basal ganglia) also believed to integrate signaling from the midbrain dopaminergic and cortical glutamatergic pathways. In schizophrenic conditions patients display dysfunction in these signaling pathways, abnormal striatal output has been implicated in the pathophysiology of the disease ^{2, 3, 4}.

It has hypothesized that inhibition of PDE10A will increase the intracellular levels of cGMP (cyclic guanosine monophosphate) and cAMP (cyclic adenosine monophosphate), thereby increasing striatal output and restoring behavioral inhibition ⁵. Disturbances of the basal ganglia processes is heavily involved in schizophrenia. Phosphodiesterase 10A (PDE10A) is a basal ganglia specific hydrolase, which plays an essential role in regulating cAMP/PKA (protein kinase A) and cGMP/PKG (protein kinase G) signaling cascades by controlling the magnitude, duration and cellular location of cAMP/cGMP elevation ⁶. Biochemical and behavioral data indicate that PDE10A inhibition activates cAMP/PKA signaling in the basal ganglia process, leading to the potentiation of dopamine D₁ receptor signaling, and concomitant inhibition of dopamine D₂ receptor signaling. Across mammalian species PDE10A is potentially expressed in the striatum the main recipient of dopaminergic afferents from the substantia nigra. Due to its high striatal expression PDE10A inhibitors are regarded as therapeutic approach in the treatment of disease related to striatal dysfunction such as Schizophrenia ^{7, 8, 9}.

The antipsychotic-like effect of PDE10A inhibitors has been proven in animal models. Preclinical evidence in a range of animal models suggests that a PDE10A inhibitor could provide efficacy on positive, cognitive and negative symptoms of schizophrenia and PDE10A inhibitors are currently being evaluated in clinical trials for the treatment of schizophrenia. Today about 20 pharmaceuticals companies have running discovery program to identification of potential PDE10A inhibitor ¹, success of identification of seven compounds by different pharmaceutical companies presently undergoing human trials. Schizophrenia remains an enigma though enhanced understanding of the cause, consequence, and potential treatments are bringing out today much light to the subject but till day considering as a lifelong mental disorder with nobody known to cure, and psychiatric practitioner worldwide believed that 1% world population affected by this severe chronic disease and it prevail in all type of classified communities.  Presently a dozen no. of drug compounds is known as efficient treatment, despite these recognized drugs are prescribed for treatment but typical and atypical antipsychotic treat only the positive symptoms of the disease and have little bit limited efficacy and tolerability resulting in high rates of discontinuation among patients, it’s make psychotherapist’s job more challengeable.

MATERIALS AND METHODS: Recently a research team of Merck Research Laboratories successfully identified a novel class of pyrazolopyrimidine to potentially active against PDE10A inhibition. This research team investigated out that PyP-1(best “pyrazolopyrimidine” identified by that team)) ¹ exhibits subnanomolar potency towards PDE10A (Ki = 0.23 nM), excellent pharmacokinetic (PK) and physicochemical properties, and a clean off-target profile of PyP-1 after a big span experimentation ¹. PyP-1 displays dose-dependent efficacy in numerous pharmacodynamics (PD) assays that measure potential for anti-psychotic activity and cognitive improvement ¹, so on this all ground we start our work with using “in silico” utilities to search for as similar to PyP-1 in a freely accessible drug like structural bank ZINCdocking.org, herein work we investigate through 180,000,000 DL molecular structures and finally left with few in hand, a long span computation performed and on the outcomes of that, considering, our reporting molecules may be a better one than pyp-1 as potentially active against PDE10A as inhibitor for treatment for Schizophrenia. We’re coming these molecular structures in front of scientific community for further investigation by any methodological approach including “in silico”.

During the past decade, increasing numbers of complex structures were solved by the development of high throughput X-ray crystallographic technique ¹⁰ and NMR¹¹ methods and it grounding the basis for “in silico” technique to get it in the proper now days shape as a very valuable intervening technique in a total drug evaluation strategy to employed and very honestly it got a respectable space in concerning communities as a big comprehensive strategic tool to intermediate in drug designing workout, getting much viable by day.

We’re initiate our work with rcsb.org.in with a download of “5DH5”, it reported in recent time, it was a crystallographic structure of pyp-1 with “in vitro” experiments in Homo sapiens phosphodiesterase PDE10A. Ramachandran plot of 5DH5 taken, it in Fig. 1(a) clearly showing that the maximum residues are in the core region (red colored) placed, very few residues are in the allowed region (dark yellow colored) and only two of the residues showing to place in disallowed region, nevertheless much fairer crystallographic structures was in our hand.

A close look on interaction pattern for pyp-1 with phosphodiesterase PDE10A bring out facts that it coordinated in two different regions in phosphodiesterase “PDE10A”, inspection pointed out that it was a homodimeric protein and in both chains have a similar kind of location where a molecule of pyp-1 has interactionally placed in each protein chain, these binding location after here referred as “1” and “2”. In both binding location pyp-1 bind up with very same efficacy, interactions are in common frame (Fig 1. (b) and (c) but the pyp-1 is in different conformation in these binding locations.

FIG. 1 (a) RAMACHANDRAN PLOT FOR “5DH5”, BINDING INTERACTIONS OF PYP-1 IN (b) REGION “1” AND (c) IN REGION “2” IN PHOSPHODIESTERASE PDE10A

RESULTS AND DISCUSSION: The potential energy (PRIME MM-GBSA) of pyp-1 in region “1” is calculated (OPLS3) out to -1683.994 and for region “2” it is -1738.587 i.e. in location “2” pyp-1 was better placed in energy stability terms, it’s may due to various reasons. The pyp-1 has three important interactions, pyrazole ring has π-π stacking with Histidine (515), it is common in both regions, however in region “2” an extra π-π stacking of pyrazole ring of pyrazolopyrimidine (pyp-1) with phenylalanine (719) makes it more efficient binding region, pyp-1 acts as two H-bond acceptor in both region, pyridine ring for tyrosine (683) and pyrimidine (pyp-1, pyrazolopyrimidine) for Glycine (716).

Above mentioned interactions, as a consideration, that are important for recognizing as similar pyp-1like molecular structures identification. We prepared the protein PDB 5DH5 with glide program in protein preparation wizard the tool is very important to raw data of protein PDB file to came it in condition to molecular docking, in protein preparation panel in maestro 5DH5 first preprocessed with default settings and this job added the Hydrogen atoms to PDB, assign bond order in protein, create zero bond order with metal atoms and disulfide bridges between individual cysteine units, after job completion came with a message “missing side chains in the protein” we ran further to add the missing side chain and after the job came with a message of position alteration of a particular amino acid which was resolved in next steps, we take a Ramachandran plot at this stage, the plot (Fig 1(a) prevails that PDB is as usual).

In a second stage of protein preparation wizard(review and modify) we have two homodimer chains A and B, both pyp-1 binding location were near to two adjacent metal (Mg²⁺, Zn²⁺) coordination sites in each chain of 5DH5, we in this stage deleted the 33 water molecules among the total of 43 water molecules present in 5DH5, which are either Hydrogen bonded or non-Hydrogen bonded with the amino acid both chains, we remains untouched a total 10 water molecules which are all present in hex dentate co-ordination sphere around two separate Mg²⁺ atoms (one ligand in them is ASP:554 of chain A and chain B in location “1” and “2”), two Zn²⁺ ions are also present adjacent to Mg²⁺ coordination sphere, which coordinated in square pyramidal coordination sphere one of them ligand i.e. a water molecule is common as a ligand to both metal coordination sphere it’s both lone pair directed towards different metals (here Mg²⁺ & Zn²⁺) to coordinating it, so it’s in a role as a bi-dentate  bridge to both metals coordination sites, these two metals at four coordination sites are very important for PDE10A quaternary and tertiary structural concerns, it’s there a great impact on the nearby active site where pyp-1 bind up in the cavity, when we checked with deleting both Zn²⁺  and  remain with two Mg²⁺ ions the docking score sank up by two unit against when it included in the same job. We generate the state for pyp-1 in binding cavity and we stood with the original state. And in the third stage (refinement) of protein preparation wizard first we run optimization job, its take about 2 minutes in 4.0 GHz Machine (Octa Core) and after completion, run for minimization job, minimization run take about 5 minutes to complete, it utilizes OPLS3 force field and with setting; converge heavy metals to RMSD 0.30Ǻ. Grid were generated in both “1” and “2” centrally defined location as ligand selection with partial charge of ligand included. We considered pyp-1 as a standard molecular drug lead’s structure and using “tanimoto” similarity measure we separated out DL molecular structures in DL molecular structure file downloaded from free accessible zincdocking.org with setting to identification of 1% similar to pyp-1, in a general such drug like molecular structure file have 140,000 structures in an average and we have performed similarity search with 131 such drug structure files (.sdf). After such jobs we left first about 183,000 DL molecular structures which were structurally very similar to pyp-1.

The job separated out 1% DL molecular structures which were best in similarity measure to pyp-1. Extracted such DL molecular structures are our raw structures for docking analysis, we prepared such extracted DL molecules in “ligprep” wizard. The LigPrep process consists of a series of steps that perform conversions, apply corrections to the structures, generate variations on the structures, eliminate unwanted structures, and optimize the structures. Many of the steps are optional and are controlled by selecting options in the LigPrep panel or by specifying command-line options in maestro. With prepared ligand and previously generated grid for binding region of pyp-1 in “1” and “2” region in phosphodiesterase PDE10A, at this instance docking was the next step for our work concerns, with each prepared ligand file (131 such prepared ligand file which were .mae typed ) we performed docking job first in “SP”(simple precession) mode in “Glide docking” with included ligand partial charge, ligand sampling unaltered and remain default “flexible” with included input ring conformation and other remaining settings were as default,  131 docking job performed. The analysis of job result manually separated out good scoring molecules which are generally better than pyp-1 in docking score, and these DL molecular structures are separated out and saved separately in a .mae file, and in this stage need to perform with extra precision docking calculation mode i.e. XP docking. Previously separated ligand in an .mae file again prepared in ligand preparation wizard, in this wizard ionized state ligand generation are also available using  “ionizer” but we haven’t much concerned with ionized ligand in present context, so only utilized “epik” for ligand preparation job and not go for “ionizer”(an another tool in ligprep job setting). In the next step docking performed in “maestro” with “glide” in “XP (extra precision) mode”, setting included “include input ring conformation” and “reward intramolecular Hydrogen bonds”.

Docking performed in both regions “1” and “2” of binding pyp-1 in PDE10A the result is much improved due to included various extra terms in XP docking mode. In performing final XP docking job, during the generating grid we used some constraints these are listed in table 1.1, in  our work have been given priorities of such interactions in our investigation, and docking performed with above constraints and finally stacked with around 2000 molecules which have XP docking score much competing or in instead, better than pyp-1. With these separated molecules quikprop Job performed, the result with the docking score and others properties (Table- 5DH5- “1” and Table-5DH5- “2” for corresponding location i.e “1” and “2” to binding of “pyp-1” in “5DH5”) cut further molecules to report i.e. requirement of properties in required limit, such as CNS activity, lipophilicity, and other important medicinal parameters also remove various structures in this context as a DLL consideration.

In both tables the DLL are in require limit of drug properties, the docking score which reflects binding efficacy are much better than the pyp-1 in the docking score, in location “1” for pyp-1it is at -9.79 and for location “2” it for that at -8.759, the difference between the DS in location “1” and “2” is around 1 unit, so some difference in binding ability. In table: 5DH5- “1” the DS for ZINC71524592 was at the highest and it was at -13.21 which is 3.5 unit more than DS of pyp-1 at the same location. The various computed out medicinal properties are also in the required limit but the lipophilic nature of ZINC71524592

TABLE 1: USED CONSTRAINTS FOR GRID GENERATION FOR REGION “1” AND FOR REGION “2” FOR PYP-1 IN “PDE10A”

(a)                                                                                       (1)

(b)                                                                                        (2)

(c)                                                                                        (3)

(d)                                                                                        (4)

(e)                                                                                        (5)

FIG. 2: IMAGES OF pyp-1(a,1), ZINC71524592(b,2), ZINC83982577(c,3), ZINC79760798(d,4) & ZINC06025953(e,5) IN DOCKED POSITION IN REGION “1” OF HOMODIMERIC PHOSPHODIESTERASE PDE10A (5DH5) AND ITS CORRESPONDING INTERACTION DIAGRAMS.

have some concerns, its far distant to pyp-1 which we have found in XP visualizer panel it at -7.1 for pyp-1 but for ZINC71524592 it was only at -6.2. On another hand, the QMDCK and QCaco values are also not too much appreciable in this venture, higher values for these terms are generally better for DLL recognition. Nevertheless interaction pattern for ZINC71524592 is much more efficient, the two interactions which we consider previous as a constraint for docking (it was always a mandatory interaction requirement during docking calculation and afterwards pose generation) in context to pyp-1 it has various other interactions including H-bonding, π-π stacking with neighboring amino acids, make it energetically most favorable in binding location in our investigation, in region “2” it also bind up with closer efficiency with a fair docking score of  -11.92.  The 2^nd and 3^rd listed molecules ZINC83982577 and ZINC79760798 respectively are binding efficiently in region “1”

but it region “2” these are loose some effectiveness in binding with docking score 4.34 and 5.23 unit less than corresponding for region “1” respectively, so it efficient only in a single site binding. But, the ZINC06025953 is the most attainable molecule (in our view), it binds up in both locations “1” and “2” very efficiently with very fair docking score of -12.38 and -10.7 respectively for these locations, almost all computed medicinal properties associated with this molecule are very fair, lipophilic nature is very important in DLL cosideration, its “Lip” score at -7.9, easily understandable it can travel through lipid bilayer smoothly with lesser opposing resistance than pyp-1(-7.1). The computed QPBB of ZINC06025953 is -0.74 that value for pyp-1 is -0.82 so very close to each other, “QMDCK”, “QCaco”, “QHERG” & “QKhsa” are very appreciable in DLL context, Predicted aqueous solubility, a very important check point in drug development procedure, herein “QlogS”, for ZINC06025953(-7.912), somewhat better computed score against pyp-1(-6.898). Metabolite for ZINC06025953 is calculated out to 4 instead 3 for pyp-1, both pyp-1 and ZINC06025953 have value -1 for CNS activity so both have same proportionate activity in this regard various properties which is no reported here due to written-space limitation concerns, are also very favorable.

The H-bonding interactions, in the interaction diagram for ZINC06025953 (Fig:2(5)) the two important interactions i.e. with TYR: 683 and GLN:716 in both locations “1”and “2” are very efficiently maintained and no other extra H-bonding interaction are present with ZINC06025953 in both locations in the phosphodiesterase, one hydrogen bond has some weakening effect but another has almost same scale strengthening itself, a mutual exchange effect so overall H-bonding stabilization maintained. On the another hand π-π stacking with ZINC06025953 has a big promotion and got very strange multi channels stacking phenomena, and in this regard, the interaction diagram (Fig. 2(5)) clearly showing that the pyp-1 stacking with PHE:719 is strictly maintained with ZINC06025953 and complex networking of π-π stacking make a big relief to energy stabilization in both locations, conclusively π-π stacking gave a direction to look much better to its favor. Nevertheless, other molecules may have good impact as a DLL consideration, scientific bodies need to look it well and also too ahead.

TABLE 2: 5DH5- “1”

(D.S.(Docking Score, kcal/mol), Lip(Lipophilicity), CNS(Predicted central nervous system activity on a, # –2 (inactive) to +2 (active) scale), dHB Estimated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution. Values are averages taken over a number of configurations, so they can be non-integer, #0.0 – 6.0), aHB Estimated number of hydrogen bonds that would be accepted by the solute from water molecules in an aqueous solution. Values are averages taken over a number of configurations, so they can be non-integer, #2.0 – 20.0, QPlogS Predicted aqueous solubility, log S. S in mol dm^–3 is the concentration of the solute in a saturated solution that is in equilibrium with the crystalline solid, #–6.5 – 0.5, QHERG (Predicted IC50 value for blockage of HERG K+ channels, #concern below –5), QCaco Predicted apparent Caco-2 cell permeability in nm/sec. Caco-2 cells are a model for the gut-blood barrier. QikProp predictions are for non-active transport, #<25 poor, >500 great, QPBB(Predicted brain/blood partition coefficient, #–3.0 – 1.2, QMDCK(Predicted apparent MDCK cell permeability in nm/sec, # <25 poor, >500 great ), QKp (Predicted skin permeability, log Kp, # –8.0 – –1.0, metab (Number of likely metabolic reactions, # 1 – 8), QKhsa(Prediction of binding to human serum albumin, # –1.5 – 1.5 ), PHOAbs(Predicted human oral absorption on 0 to 100% scale, # >80% is high, <25% is poor, “#” indicates Range or recommended values

TABLE 3: 5DH5- “2”

CONCLUSION: Synthesis of ZINC06025953 (i.e. 2-(3-isobutoxyphenyl) - N - (pyridin-2 ylmethyl) quinoline-4-carboxamide) is a need and above facts to verified in real manner be in demand conclusively.

ACKNOWLEDGEMENTS: The authors wish to thank with proud and privilege to Will Richard, Raghu Rangaswamy and Vinod Dewarjee of Schrodinger Ltd. for providing the Schrodinger Suite Software and its training.

Note: This research article only for academic purposes, authors not interested for any financial beneficiary.

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    How to cite this article:

    Rituraj and Srivastava KK: Schizophrenia: A Look Forward With Zinc06025953. Int J Pharm Sci Res 2017; 8(5): 2122-33.doi: 10.13040/IJPSR.0975-8232.8(5).2122-33.

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