Integrated molecular docking, 3D QSAR and molecular dynamics simulation studies on indole derivatives for designing new Pim-1 inhibitors.

Pim-1 is one of the isoforms of pim proteins comprising pim-1, pim-2 and pim-3. It was basically recognized as proviral integration moloney murine leukemia virus which is associated with T-cell lymphomogenesis. Pim-1 is known to play a crucial role in cell cycle progression and acts as downstream target for the JAK/STAT signaling pathway. Recently it has emerged as a hopeful therapeutic target for cancer treatment as deregulation or over expression of pim causes hematologic cancers. In present article molecular docking based three dimensional quantitative structure and activity relationship and molecular dynamics simulation studies have been carried out on indole derivatives reported as pim-1 inhibitors. Initially docking was carried out to obtain the receptor specific orientation of the molecules and later to understand the structural requirements of pim-1 inhibitors robust 3 D QSAR models were built using CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) methods. The reliability of the models was established from conventional (r2) and cross validated (q2) values of 0.982, 0.524 for CoMFA and 0.974, 0.586 for CoMSIA respectively. Further the predictive ability of the model was evaluated using a test set of 17 molecules. The docking studies revealed that interaction with Glu 121 is vital for binding of inhibitors to pim-1. Based on the outcome of the results new molecules with improved activity were designed. Furthermore, MD simulations were also performed to examine the stability of interactions and investigate the pivotal role of Glu 121.

Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120.

Attachment of envelope glycoprotein gp120 to the host cell receptor CD4 is the first step during the human immunodeficiency virus-1 (HIV-1) entry into the host cells that makes it a promising target for drug design. To elucidate the crucial three dimensional (3D) structural features of reported HIV-1 gp120 CD4 binding inhibitors, 3D pharmacophores were generated and receptor based approach was employed to quantify these structural features. A four-partial least square factor model with good statistics and predictive ability was generated for the dataset of 100 molecules. To further ascertain the structural requirement for gp120-CD4 binding inhibition, molecular interaction studies of inhibitors with gp120 was carried out by performing molecular docking using Glide 5.6. Based on these studies, structural requirements were drawn and new molecules were designed accordingly to yield new sulphonamides derivatives. A water based green synthetic approach was adopted to obtain these compounds which were evaluated for their HIV-1 gp120 CD4 binding inhibition. The newly synthesized compounds exhibited remarkable activity (10-fold increase) when compared with the standard BMS 806. Further the stability of newly synthesized derivatives with HIV-1 gp120 was also investigated through molecular dynamics simulation studies. This provides a proof of concept for molecular modeling based design of new inhibitors for inhibition of HIV-1 gp120 CD4 interaction.

One-pot synthesis, biological evaluation and molecular docking studies of fused thiazolo[2,3-b]pyrimidinone-pyrazolylcoumarin hybrids.

As a part of our endeavor toward the synthesis of a new class of biologically potent heterocyclic hybrids, a series of newly fused thiazolo[2,3-b]pyrimidinones bearing a pyrazolylcoumarin moiety (6a-p) were synthesized in acceptable yields. Anticipated structures of all titled compounds were in agreement with spectral and analytical (C, H and N) analyses. The compounds were screened for in vitro antibacterial activity against both G+ and G- bacterial strains and antiproliferative activity against K562 (chronic myelogenous leukemia), MCF-7 (breast cancer), MDA-MB-231 (breast cancer), COLO 205 (colorectal adenocarcinoma), HepG2 (hepatocellular carcinoma) cell lines. Further, potent antibacterial compounds were subjected to molecular docking studies in order to gain insight into their plausible binding modes and mechanism of action against MurB. The modeling results were in agreement with the experimental data.

Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.

The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔGbind and experimental pIC50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

An integrated molecular modeling approach for in silico design of new tetracyclic derivatives as ALK inhibitors.

Anaplastic lymphoma kinase (ALK), a promising therapeutic target for treatment of human cancers, is a receptor tyrosine kinase that instigates the activation of several signal transduction pathways. In the present study, in silico methods have been employed in order to explore the structural features and functionalities of a series of tetracyclic derivatives displaying potent inhibitory activity toward ALK. Initially docking was performed using GLIDE 5.6 to probe the bioactive conformation of all the compounds and to understand the binding modes of inhibitors. The docking results revealed that ligand interaction with Met 1199 plays a crucial role in binding of inhibitors to ALK. Further to establish a robust 3D-QSAR model using CoMFA and CoMSIA methods, the whole dataset was divided into three splits. Model obtained from Split 3 showed high accuracy ([Formula: see text] of 0.700 and 0.682, [Formula: see text] of 0.971 and 0.974, [Formula: see text] of 0.673 and 0.811, respectively for CoMFA and CoMSIA). The key structural requirements for enhancing the inhibitory activity were derived from CoMFA and CoMSIA contours in combination with site map analysis. Substituting small electronegative groups at Position 8 by replacing either morpholine or piperidine rings and maintaining hydrophobic character at Position 9 in tetracyclic derivatives can enhance the inhibitory potential. Finally, we performed molecular dynamics simulations in order to investigate the stability of protein ligand interactions and MM/GBSA calculations to compare binding free energies of co-crystal ligand and newly designed molecule N1. Based on the coherence of outcome of various molecular modeling studies, a set of 11 new molecules having potential predicted inhibitory activity were designed.