scholarly journals Deuteration and Inhibitor Binding Dependence of Protein Collective Vibrations

2019 ◽  
Vol 116 (3) ◽  
pp. 488a
Author(s):  
Yanting Deng ◽  
Jeffrey Mckinney ◽  
Andrea Markelz
2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Analise C. Doney ◽  
Steven Wheeler

<p>Despite the ubiquity of stacking interactions between heterocycles and aromatic amino acids in biological systems, our ability to predict their strength, even qualitatively, is limited. Based on rigorous <i>ab initio</i> data, we have devised a simple predictive model of the strength of stacking interactions between heterocycles commonly found in biologically active molecules and the amino acid side chains Phe, Tyr, and Trp. This model provides rapid predictions of the stacking ability of a given heterocycle based on readily-computed heterocycle descriptors. We show that the values of these descriptors, and therefore the strength of stacking interactions with aromatic amino acid side chains, follow simple predictable trends and can be modulated by changing the number and distribution of heteroatoms within the heterocycle. This provides a simple conceptual model for understanding stacking interactions in protein binding sites and optimizing inhibitor binding in drug design.</p>


2019 ◽  
Vol 25 (42) ◽  
pp. 5803-5821 ◽  
Author(s):  
Mona N. Rahman ◽  
Dragic Vukomanovic ◽  
Jason Z. Vlahakis ◽  
Walter A. Szarek ◽  
Kanji Nakatsu ◽  
...  

The development of isozyme-selective heme oxygenase (HO) inhibitors promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. It is already known that HO has cytoprotective properties with a role in several disease states; thus, it is an enticing therapeutic target. Historically, the metalloporphyrins have been used as competitive HO inhibitors based on their structural similarity to the substrate, heme. However, heme’s important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), results in non-selectivity being an unfortunate side effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort over a decade ago to develop novel compounds as potent, selective inhibitors of HO. The result was the creation of the first generation of non-porphyrin based, non-competitive inhibitors with selectivity for HO, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated and provided insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies. Notably, HO-1 inhibitors are of particular interest for the treatment of hyperbilirubinemia and certain types of cancer. Key features based on this initial study have already been used by others to discover additional potential HO-1 inhibitors. Moreover, studies have begun to use selected compounds and determine their effects in some disease models.


2020 ◽  
Vol 20 (11) ◽  
pp. 1017-1030
Author(s):  
Haonan Zhang ◽  
Zhengquan Gao ◽  
Chunxiao Meng ◽  
Xiangqian Li ◽  
Dayong Shi

Protein tyrosine phosphatase 2 (SHP-2) has long been proposed as a cancer drug target. Several small-molecule compounds with different mechanisms of SHP-2 inhibition have been reported, but none are commercially available. Pool selectivity over protein tyrosine phosphatase 1 (SHP-1) and a lack of cellular activity have hindered the development of selective SHP-2 inhibitors. In this review, we describe the binding modes of existing inhibitors and SHP-2 binding sites, summarize the characteristics of the sites involved in selectivity, and identify the suitable groups for interaction with the binding sites.


1987 ◽  
Vol 42 (6) ◽  
pp. 684-689 ◽  
Author(s):  
John L. Huppatz ◽  
John N. Phillips

Optically active α-methylbenzylamino 2-cyanoacrylic esters were synthesized and assayed as inhibitors of the Hill reaction in isolated pea chloroplast fragments. The 5-isomers were more potent inhibitors than the S-isomers with discriminations of from ten to greater than 100-fold being observed. A β-alkyl substituent in the cyanoacrylate molecule affected both the level of activity and the difference in activity between the isomers. An α,α-dimethylbenzylamino derivative was also active at about the same level as the corresponding α-methylbenzylamino racemate. This result could be explained in terms of the orientation of the phenyl ring in the receptor site. Replacement of the α-methylbenzylamino group by other α-alkyl and α-phenyl substituents had little effect on activity. However, an α-benzyl group was beneficial.


2020 ◽  
Vol 18 (16) ◽  
pp. 3069-3081 ◽  
Author(s):  
Maria G. Khrenova ◽  
Anna M. Kulakova ◽  
Alexander V. Nemukhin

Comprehensive molecular modeling and kinetic analysis reveal a novel mechanism of the inhibition of the oncogenic mutant of the “undruggable” KRAS protein.


2021 ◽  
Vol 120 (3) ◽  
pp. 204a-205a
Author(s):  
Anna Pavlova ◽  
Diane L. Lynch ◽  
Micholas Dean Smith ◽  
Jeremy D. Smith ◽  
James C. Gumbart

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