In-house Molecule Research Articles

Binary quantitative activity-activity relationship (QAAR) studies to explore selective HDAC8 inhibitors: In light of mathematical models, DFT-based calculation and molecular dynamic simulation studies

Histone deacetylase 8 (HDAC8) selectivity over other HDACs is a major concern of interest, since HDAC8 has been implicated as a potential drug target of many diseases including haematological malignancy. Quantitative activity-activity relationship (QAAR) study is a good strategy to explore the possible features to design HDAC8 selective inhibitors. Here, a mathematical framework has been constructed to understand the important molecular fragments responsible for HDAC8 selectivity over HDAC1, 2 and 3. This study also deals with binary QAAR-based HDAC8 selectivity screening of some in-house molecules and understanding the toxicity of the in-house molecules using DFT-based descriptors. Further, this study explores the possible binding mechanism of in-house compounds with HDAC8 by molecular dynamic simulation. Hence, the comparative learning amongst the mathematical models, DFT-based calculation and molecular dynamic simulation methods will surely enrich the scientific community to design selective HDAC8 inhibitors in future.

An in-silico approach to identify the potential hot spots in SARS-CoV-2 spike RBD to block the interaction with ACE2 receptor

A novel acute viral pneumonia induced by SARS-CoV-2 exploded at the end of 2019, causing a severe medical and economic crisis. For developing specific pharmacotherapy against SARS-CoV-2, an in silico virtual screening was developed for the available in-house molecules. The conserved domain analysis was performed to identify the highly conserved and exposed amino acid regions in the SARS-CoV-2-S RBD sites. The Protein-Protein interaction analyses demonstrated the higher affinity between the SARS-CoV-2-S and ACE2 due to varieties of significant interactions between them. The computational alanine scanning mutation study has recognized the highly stabilized amino acids in the SARS-CoV-2-S RBD/ACE2 complex. The cumulative sequence investigations have inferred that Lys417, Phe486, Asn487, Tyr489, and Gln493 are perhaps the iconic target amino acids to develop a drug molecule or vaccine against SARS-CoV-2 infection. Most of the selected compounds include luteolin, zhebeirine, 3-dehydroverticine, embelin, andrographolide, ophiopogonin D, crocin-1, sprengerinin A, B, C, peimine, etc. were exhibited distinguish drug actions through the strong hydrogen bonding with the hot spots of the RBD. Besides, the 100 ns molecular dynamics simulation and free energy binding analysis showed the significant efficacy of luteolin to inhibit the infection of SARS-CoV-2. Communicated by Ramaswamy H. Sarma

Quantification of Drugs in Distinctly Separated Ocular Substructures of Albino and Pigmented Rats.

The rat is a commonly used species in ocular drug research. Detailed methods of separating rat ocular tissues have not been described in literature. To understand the intraocular drug distribution, we developed a robust method for the separation of individual anterior and posterior substructures of pigmented Brown Norway (BN) and albino Wistar Han (WH) rat eyes, followed by quantification of drug concentration in these substructures. A short formalin incubation, which did not interfere with drug quantification, enabled the preservation of individual tissue sections while minimizing cross-tissue contamination, as demonstrated by histological analysis. Following oral administration, we applied the tissue separation method, in order to determine the ocular concentrations of dexamethasone and levofloxacin, as well as two in-house molecules BI 113823 and BI 1026706, compounds differing in their melanin binding. The inter-individual variability in tissue partitioning coefficients (Kp) was low, demonstrating the reproducibility of the separation method. Kp values of individual tissues varied up to 100-fold in WH and up to 46,000-fold in BN rats highlighting the importance of measuring concentration directly from the ocular tissue of interest. Additionally, clear differences were observed in the BN rat tissue partitioning compared to the WH rat. Overall, the developed method enables a reliable determination of small molecule drug concentrations in ocular tissues to support ocular drug research and development.

Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of some in-house molecules as papain-like protease (PLpro) inhibitors

World Health Organization characterized novel coronavirus disease (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) as world pandemic. This infection has been spreading alarmingly by causing huge social and economic disruption. In order to response quickly, the inhibitors already designed against different targets of previous human coronavirus infections will be a great starting point for anti-SARS-CoV-2 inhibitors. In this study, our approach integrates different ligand based drug design strategies of some in-house chemicals. The study design was composed of some major aspects: (a) classification QSAR based data mining of diverse SARS-CoV papain-like protease (PLpro) inhibitors, (b) QSAR based virtual screening (VS) to identify in-house molecules that could be effective against putative target SARS-CoV PLpro and (c) finally validation of hits through receptor-ligand interaction analysis. This approach could be used to aid in the process of COVID-19 drug discovery. It will introduce key concepts, set the stage for QSAR based screening of active molecules against putative SARS-CoV-2 PLpro enzyme. Moreover, the QSAR models reported here would be of further use to screen large database. This study will assume that the reader is approaching the field of QSAR and molecular docking based drug discovery against SARS-CoV-2 PLpro with little prior knowledge. Communicated by Ramaswamy H. Sarma

De-Risking Early-Stage Drug Development With a Bespoke Lattice Energy Predictive Model: A Materials Science Informatics Approach to Address Challenges Associated With a Diverse Chemical Space

The solid-state properties of new chemical entities are critical to the stability and bioavailability of pharmaceutical drug products. The stability of the solid-state packing is described by the packing energy and an accurate prediction of this property for drug molecules would therefore be desirable. However, this has been difficult to achieve because of the lack of fundamental thermodynamic data on drug molecules. A potential solution would be to use calculated lattice energies to build a model and design molecules with desired physicochemical properties from an early stage, aligning with a “design by first intent” strategy for physicochemical properties. We first demonstrate the high correlation and interchangeability between QSPR models built using calculated lattice energies and experimental sublimation enthalpies for small organic molecules. We then present a QSPR model trained on in-house molecules using lattice energies calculated from crystal structures. The result is a model that enables fast prediction of the lattice energies of in-house molecules from 2-D molecular structure with reasonable accuracy (R2 = 0.92, root mean square error = 3.58 kcal/mol). We explore the model elements to improve our understanding of the molecular properties that contribute to lattice energy and then suggest potential cross-industry aspects that may enhance the application of the concept.

Discovery of a highly selective FLT3 inhibitor with specific proliferation inhibition against AML cells harboring FLT3-ITD mutation

FLT3 is often over-expressed in AML, and FLT3 mutants, especially FLT-ITD, are closely related to the poor prognosis in AML patients. Thus, FLT3 has become an attractive target for AML therapy. A series of FLT3 inhibitors have been evaluated in various clinical trials, one of which was approved for AML. However, current FLT3 inhibitors still faced the challenges of kinase selectivity and drug resistance due to concurrent FLT3-ITD-TKD mutations. In this work, a new FLT3 inhibitor (compound 1) with simple structure was discovered through virtually screening an in-house molecule database which contains numerous compounds with kinase-inhibition activity. Compound 1 was identified with potent inhibitory activity against several FLT3 mutants and high FLT3 selectivity over other kinases. Moreover, its anti-growth effects on tumor cells in vitro were dependent on the expression of FLT3-ITD, and it showed little cytotoxicity to MV4-11 and human normal cells. Mechanism studies illustrated that compound 1 blocked FLT3 pathway, caused cell cycle arrest and induced apoptosis in MV4-11 cells. Finally, the binding mode of compound 1 was studied by molecular dynamics simulations, which provides insights into key residues involved in intermolecular binding and further structural optimization strategy. Compound 1 can thus serve as a good starting point for the research on FLT3 inhibitors towards the kinase selectivity and potential to overcome drug resistance.

Development of a novel noncapillary plasma microsampling device for ultra-low volume of blood collection.

The desire for serial microsampling in mice has led to extensive research in this field within the pharmaceutical industry. The ability to profile a compound's in vivo properties with less material and fewer mice has obvious advantages. A new device and workflow was developed at the Takeda Oncology site to allow scientists to isolate plasma from very low volumes of mouse blood (as low as 20 μl) collected using standard microsampling techniques. A side-by-side in vitro comparison of plasma concentrations was performed using this new device and conventional sampling methods with commercial and in-house molecules. The plasma concentrations of the molecules tested were very consistent between the conventional sampling techniques and this new device/workflow. In addition, several in-life studies have also been conducted to validate this new technique as a primary PK screening tool at the Takeda Boston. The new device is simple to use and very cost effective with the added benefit that no additional training is needed for the animal technicians and the same centrifuge equipment can be employed. This device can be used for blood volumes ranging from 20 to 100 μl enabling studies not just in rat and dog but more importantly in mice.