In Silico Rational Design and Protein Engineering of Disulfide Bridges of an α‐Amylase from Geobacillus sp. to Improve Thermostability

2021 ◽  
pp. 2000274
Author(s):  
Heng Zhang ◽  
Wenxin Zhai ◽  
Lin Lin ◽  
Ping Wang ◽  
Xiangyang Xu ◽  
...  
Keyword(s):  
Protein Engineering ◽  
In Silico ◽  
Rational Design ◽  
Disulfide Bridges

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

scholarly journals Rational design of potent anti-COVID-19 main protease drugs: An extensive multi-spectrum in silico approach

2021 ◽  
Vol 330 ◽  
pp. 115636
Author(s):  
Sajjad Ahmad ◽  
Yasir Waheed ◽  
Saba Ismail ◽  
Muzammil Hasan Najmi ◽  
Jawad Khaliq Ansari
Keyword(s):  
In Silico ◽  
Rational Design ◽  
Main Protease

Rational Design of Macrolides by Virtual Screening of Combinatorial Libraries Generated through in Silico Manipulation of Polyketide Synthases

2006 ◽  
Vol 49 (6) ◽  
pp. 2077-2087 ◽  
Author(s):  
Sergey B. Zotchev ◽  
Alla V. Stepanchikova ◽  
Anastasia P. Sergeyko ◽  
Boris N. Sobolev ◽  
Dmitrii A. Filimonov ◽  
...  
Keyword(s):  
Virtual Screening ◽  
In Silico ◽  
Rational Design ◽  
Combinatorial Libraries ◽  
Polyketide Synthases

Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase

2016 ◽  
pp. 249-277
Author(s):  
Sailu Sarvagalla ◽  
Mohane Selvaraj Coumar
Keyword(s):  
Protein Interactions ◽  
In Silico ◽  
Rational Design ◽  
Kinase Activity ◽  
Hot Spot ◽  
Binding Pocket ◽  
Atp Binding ◽  
Protein Protein Interactions ◽  
Structure Based Drug Design ◽  
Atp Binding Site

Most of the developed kinase inhibitor drugs are ATP competitive and suffer from drawbacks such as off-target kinase activity, development of resistance due to mutation in the ATP binding pocket and unfavorable intellectual property situations. Besides the ATP binding pocket, protein kinases have binding sites that are involved in Protein-Protein Interactions (PPIs); these PPIs directly or indirectly regulate the protein kinase activity. Of recent, small molecule inhibitors of PPIs are emerging as an alternative to ATP competitive agents. Rational design of inhibitors for kinase PPIs could be carried out using molecular modeling techniques. In silico tools available for the prediction of hot spot residues and cavities at the PPI sites and the means to utilize this information for the identification of inhibitors are discussed. Moreover, in silico studies to target the Aurora B-INCENP PPI sites are discussed in context. Overall, this chapter provides detailed in silico strategies that are available to the researchers for carrying out structure-based drug design of PPI inhibitors.

scholarly journals Genetically Engineered Proteins to Improve Biomass Conversion: New Advances and Challenges for Tailoring Biocatalysts

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2879 ◽  
Author(s):  
Lucas Ferreira Ribeiro ◽  
Vanesa Amarelle ◽  
Luana de Fátima Alves ◽  
Guilherme Marcelino Viana de Siqueira ◽  
Gabriel Lencioni Lovate ◽  
...  
Keyword(s):  
Protein Engineering ◽  
Rational Design ◽  
Biomass Conversion ◽  
Low Cost ◽  
Catalytic Performance ◽  
Genetically Engineered ◽  
Production Lines ◽  
Current Application ◽  
Powerful Approach

Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass are being used for the production of biofuels and fine chemicals. Since most of the enzymes used in the biorefinery industry act in suboptimal conditions, modification of their catalytic properties through protein rational design and in vitro evolution techniques allows the improvement of enzymatic parameters such as specificity, activity, efficiency, secretability, and stability, leading to better yields in the production lines. This review focuses on the current application of protein engineering techniques for improving the catalytic performance of enzymes used to break down lignocellulosic polymers. We discuss the use of both classical and modern methods reported in the literature in the last five years that allowed the boosting of biocatalysts for biomass degradation.

scholarly journals A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI

2020 ◽  
Vol 13 (11) ◽  
pp. 338
Author(s):  
Joanna Bojarska ◽  
Milan Remko ◽  
Martin Breza ◽  
Izabela Madura ◽  
Andrzej Fruziński ◽  
...  
Keyword(s):  
Drug Design ◽  
In Silico ◽  
Rational Design ◽  
Enzyme Inhibitors ◽  
Building Blocks ◽  
Angiotensin Converting Enzyme Inhibitors ◽  
Converting Enzyme Inhibitors ◽  
Supramolecular Synthons ◽  
Comprehensive Classification ◽  
Proline Derivatives

Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO−), -N+ and -COOH(-COO−), -NH and -COOH(-COO−), -NH+ and -COOH(-COO−), and -NH2+ and -COOH(-COO−). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.

In silico rational design and virtual screening of antixoidant tripeptides based on 3D-QSAR modeling

2019 ◽  
Vol 1193 ◽  
pp. 223-230 ◽  
Author(s):  
Haiqiong Guo ◽  
Yuxuan Wang ◽  
Qingxiu He ◽  
Yuping Zhang ◽  
Yong Hu ◽  
...  
Keyword(s):  
Virtual Screening ◽  
In Silico ◽  
Rational Design ◽  
3D Qsar ◽  
Qsar Modeling
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