Molecular Modeling Studies on the Binding Mode of the PD-1/PD-L1 Complex Inhibitors

The programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) is an immune checkpoint (ICP) overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. To determine important residues for ligand binding, we applied molecular docking studies to PD-1/PD-L1 complex inhibitors against the PD-L1 protein. Our data revealed that the residues Tyr56, Asp122, and Lys124 play critical roles in ligand binding to the PD-L1 protein and they could be used to design ligands that are active against the PD-1/PD-L1 complex. The formation of H-bonds with Arg125 of the PD-L1 protein may enhance the potency of the PD-1/PD-L1 binding

Computational studies and peptidomimetic design for the human p53–MDM2 complex

The interaction between human p53 and MDM2 is a key event in controlling cell growth. Many studies have suggested that a p53 mimic would be sufficient to inhibit MDM2 to reduce cell growth in cancerous tissue. In order to design a potent p53 mimic, molecular dynamics (MD) simulations were used to examine the binding interface and the effect of mutating key residues in the human p53–MDM2 complex. The Generalized Born surface area (GBSA) method was used to estimate free energies of binding, and a computational alanine-scanning approach was used to calculate the relative effects in the free energy of binding for key mutations. Our calculations determine the free energy of binding for a model p53–MDM2 complex to be −7.4 kcal/mol, which is in very good agreement with the experimentally determined values (−6.6–−8.8 kcal/mol). The alanine-scanning results are in good agreement with experimental data and calculations by other groups. We have used the information from our studies of human p53–MDM2 to design a Β-peptide mimic of p53. MD simulations of the mimic bound to MDM2 estimate a free energy of binding of −8.8 kcal/mol. We have also applied alanine scanning to the mimic–MDM2 complex and reveal which mutations are most likely to alter the binding affinity, possibly giving rise to escape mutants. The mimic was compared to nutlins, a new class of inhibitors that block the formation of the p53–MDM2 complex. There are interesting similarities between the nutlins and our mimic, and the differences point to ways that both inhibitors may be improved. Finally, an additional hydrophobic pocket is noted in the interior of MDM2. It may be possible to design new inhibitors to take advantage of that pocket. Proteins 2005. © 2004 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34979/1/20275_ftp.pd

Conformational Studies of Glucose Transporter 1 (GLUT1) as an Anticancer Drug Target

Glucose transporter 1 (GLUT1) is a facilitative glucose transporter overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. GLUT1 works through conformational switching from an outward-open (OOP) to an inward-open (IOP) conformation passing through an occluded conformation. It is critical to determine which conformation is preferred by bound ligands because the success of structure-based drug design depends on the appropriate starting conformation of the target protein. To find out the most favorable GLUT 1 conformation for ligand binding, we ran systemic molecular docking studies for different conformations of GLUT1 using known GLUT1 inhibitors. Our data revealed that the IOP is the preferred conformation and that residues Phe291, Phe379, Glu380, Trp388, and Trp412 may play critical roles in ligand binding to GLUT1. Our data suggests that conformational differences in these five amino acids in the different conformers of GLUT1 may be used to design ligands that inhibit GLUT1

Molecular Modeling of Allosteric Site of Isoform-Specific Inhibition of the Peroxisome Proliferator-Activated Receptor PPARγ

The peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor and controls a number of gene expressions. The ligand binding domain (LBD) of PPARγ is large and involves two binding sites: orthosteric and allosteric binding sites. Increased evidence has shown that PPARγ is an oncogene and thus the PPARγ antagonists have potential as anticancer agents. In this paper, we use Glide Dock approach to determine which binding site, orthosteric or allosteric, would be a preferred pocket for PPARγ antagonist binding, though antidiabetic drugs such as thiazolidinediones (TZDs) bind to the orthosteric site. The Glide Dock results show that the binding of PPARγ antagonists at the allosteric site yielded results that were much closer to the experimental data than at the orthosteric site. The PPARγ antagonists seem to selectively bind to residues Lys265, Ser342 and Arg288 at the allosteric binding site, whereas PPARγ agonists would selectively bind to residues Leu228, Phe363, and His449, though Phe282 and Lys367 may also play a role for agonist binding at the orthosteric binding pocket. This finding will provide new perspectives in the design and optimization of selective and potent PPARγ antagonists or agonists

Encyclopedia of Pharmaceutical Science and Technology, Six Volume Set

The following contributions were made to the encyclopedia by HZ Zhong (UNO faculty) and JP Bowen: Zhong HZ, and Bowen JP. Computer-assisted drug design, pp. 620-633. Bowen JP and Zhong HZ. Computational Chemistry, pp. 600-614. Pharmaceutical science deals with the whole spectrum of drug development from start to finish. There are many different facets to the pharmaceutical industry, from initial research to the finished product, including the equipment used, trials performed, and regulations that must be followed. Presenting an overview of all of these different aspects, the Encyclopedia of Pharmaceutical Science and Technology, Fourth Edition is a must-have reference guide for all laboratories and libraries in the pharmaceutical field. Bringing together leaders from every specialty related to pharmaceutical science and technology, this is the single-source reference at the forefront of pharmaceutical R&D.The strength of this work is not only its breadth but also the caliber of contributing writers, all experts in their field, writing on all aspects of pharmaceutical science and technology. The fourth edition offers 29 new chapters ranging from biomarkers, computational chemistry, and contamination control to high-throughput screening, orally disintegrating tablets, and quality by design. The encyclopedia details best practices of equipment used, methods for manufacturing, options for packaging, and routes for drug delivery. The volumes also provide a thorough understanding of the choices behind each method. In addition, the regulations, safety aspects, patent guidance, and methods of analysis are presented.Key Areas Covered: Analytics Biomarkers Dosage forms Drug delivery Formulation Informatics Manufacturing Packaging Processing Regulatory affairs Systems validation This is an authoritative reference source for those practicing in any area of pharmaceutical science and technology, enabling the pharmaceutical specialist and novice alike to keep abreast of developments in this constantly evolving and highly competitive field.https://digitalcommons.unomaha.edu/chemfacbooks/1001/thumbnail.jp

Molecular Modeling Studies on the Binding Mode of the PD-1/PD-L1 Complex Inhibitors

The programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) is an immune checkpoint (ICP) overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. To determine important residues for ligand binding, we applied molecular docking studies to PD-1/PD-L1 complex inhibitors against the PD-L1 protein. Our data revealed that the residues Tyr56, Asp122, and Lys124 play critical roles in ligand binding to the PD-L1 protein and they could be used to design ligands that are active against the PD-1/PD-L1 complex. The formation of H-bonds with Arg125 of the PD-L1 protein may enhance the potency of the PD-1/PD-L1 binding

Drug Delivery: Fundamentals and Applications, Second Edition

Zhong HA, Güner OF, Bowen JP. Book Chapter, Chapter 20, Rational Drug Discovery, Design, and Development (pages 443-464). This book provides a comprehensive introduction to advanced drug delivery and targeting, covering their principles, current applications, and potential future developments. This edition has been updated to reflect significant trends and cutting-edge advances that have occurred since the first edition was published. All the original chapters have been retained, but the material therein has been updated. Eight new chapters have been added that deal with entirely new technologies and approaches.https://digitalcommons.unomaha.edu/chemfacbooks/1000/thumbnail.jp

Binding Selectivity Studies of Phosphoinositide 3‑Kinases Using Free Energy Calculations

Phosphoinositide 3-kinases (PI3Ks) and their phosphatidylinositol 3,4,5-triphosphate (PIP₃) products regulate a variety of cellular processes. Of these, PI3Kα is an attractive target for anticancer drug design. Mutations in the PI3Kα kinase domain alter the mobility of the activation loop resulting in gain of function. We employed molecular dynamics (MD) simulations-based energetic analysis using molecular mechanics/generalized born surface area (MM/GBSA) for PI3Kα and -γ. MD simulations were carried out for PI3K models based on the RESP (restrained electrostatic potential) and quantum mechanics (QM)-polarized ligand docking (QPLD)-derived partial charges. Computational alanine scanning was also used to evaluate the contributions of key binding residues to ligand binding. Our results show that both RESP and QPLD charge models of PI3Kα and PI3Kγ provide similar performance in MD simulations. For example, the predicted RESP and QPLD free energies of −9.5 and −9.3 kcal/mol for LY294002 binding to PI3Kγ and −10.9 and −11.7 kcal/mol for wortmannin binding to PI3Kα are in good agreement with experimental values. A significant loss in binding free energy was observed when hydrophobic residues were mutated to alanine, suggesting that specific hydrophobic interactions are important to optimal ligand binding. MM/GBSA calculations suggested that residues Ser774, Gln859, and Ile932 of PI3Kα might be used to design H1047R mutant-specific ligands, whereas Lys890 of PI3Kγ can be used for ligand design targeting PI3Kγ

Failure of Oxysterols Such as Lanosterol to Restore Lens Clarity from Cataracts

The paradigm that cataracts are irreversible and that vision from cataracts can only be restored through surgery has recently been challenged by reports that oxysterols such as lanosterol and 25-hydroxycholesterol can restore vision by binding to αB-crystallin chaperone protein to dissolve or disaggregate lenticular opacities. To confirm this premise, in vitro rat lens studies along with human lens protein solubilization studies were conducted. Cataracts were induced in viable rat lenses cultured for 48 hours in TC-199 bicarbonate media through physical trauma, 10 mM ouabain as Na+/K+ ATPase ion transport inhibitor, or 1 mM of an experimental compound that induces water influx into the lens. Subsequent 48-hour incubation with 15 mM of lanosterol liposomes failed to either reverse these lens opacities or prevent the further progression of cataracts to the nuclear stage. Similarly, 3-day incubation of 47-year old human lenses in media containing 0.20 mM lanosterol or 60-year-old human lenses in 0.25 and 0.50 mM 25-hydroxycholesterol failed to increase the levels of soluble lens proteins or decrease the levels of insoluble lens proteins. These binding studies were followed up with in silico binding studies of lanosterol, 25-hydroxycholesterol, and ATP as a control to two wild type (2WJ7 and 2KLR) and one R120G mutant (2Y1Z) αB-crystallins using standard MOETM (Molecular Operating Environment) and Schrödinger’s Maestro software. Results confirmed that compared to ATP, both oxysterols failed to reach the acceptable threshold binding scores for good predictive binding to the αB-crystallins. In summary, all three studies failed to provide evidence that lanosterol or 25-hydroxycholesterol have either anti-cataractogenic activity or bind aggregated lens protein to dissolve cataracts