A Novel Approach for the Virtual Screening and Rational Design of Anticancer Compounds

2000 ◽  
Vol 43 (10) ◽  
pp. 1975-1985 ◽  
Author(s):  
Ernesto Estrada ◽  
Eugenio Uriarte ◽  
Alina Montero ◽  
Marta Teijeira ◽  
Lourdes Santana ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Rational Design ◽  
Anticancer Compounds ◽  
Novel Approach

scholarly journals Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 198
Author(s):  
Lijun Lang ◽  
Alberto Perez
Keyword(s):  
Bayesian Inference ◽  
Virtual Screening ◽  
Statistical Mechanics ◽  
Small Molecules ◽  
Rational Design ◽  
Driving Forces ◽  
Peptide Inhibitors ◽  
Atomistic Simulations ◽  
Binding Mechanism ◽  
Intrinsically Disordered

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).

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

Rational design of inhibitors against LpxA protein of Acinetobacter baumannii using a virtual screening method

2021 ◽  
pp. 100319
Author(s):  
Sepideh Fereshteh ◽  
Hourieh Kalhor ◽  
Amin Sepehr ◽  
Hamzeh Rahimi ◽  
Mahdi Zafari ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Acinetobacter Baumannii ◽  
Rational Design ◽  
Screening Method

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

scholarly journals Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5808
Author(s):  
Marko Jukič ◽  
Dušanka Janežič ◽  
Urban Bren
Keyword(s):  
Virtual Screening ◽  
Interaction Energy ◽  
Binding Free Energy ◽  
Conformational Space ◽  
Binding Modes ◽  
Linear Interaction ◽  
Linear Interaction Energy ◽  
Ensemble Docking ◽  
Novel Approach ◽  
Screening Study

SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CLpro or Mpro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CLpro active site. These compounds will facilitate further 3CLpro inhibitor design.

scholarly journals Multivariate analysis applied to Raman mapping of dye-functionalized carbon nanotubes: a novel approach to support the rational design of functional nanostructures

The Analyst ◽  
2015 ◽  
Vol 140 (16) ◽  
pp. 5754-5763 ◽  
Author(s):  
Sonja Visentin ◽  
Nadia Barbero ◽  
Francesca Romana Bertani ◽  
Mariangela Cestelli Guidi ◽  
Giuseppe Ermondi ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Multivariate Analysis ◽  
Rational Design ◽  
Raman Mapping ◽  
Routine Test ◽  
Functionalized Carbon Nanotubes ◽  
Functional Nanostructures ◽  
Novel Approach ◽  
Reliable Classification

A powerful routine test proposed for the rational design of functional nanostructures allows fast and reliable classification of differently treated CNTs.

scholarly journals Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual Screening and Free Energy-Based Approach

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e110884 ◽  
Author(s):  
Zhe Zhang ◽  
Virginie Martiny ◽  
David Lagorce ◽  
Yoshihiko Ikeguchi ◽  
Emil Alexov ◽  
...  
Keyword(s):  
Free Energy ◽  
Virtual Screening ◽  
Small Molecule ◽  
Rational Design ◽  
Spermine Synthase

Network pharmacology-based virtual screening of natural products from Clerodendrum species for identification of novel anti-cancer therapeutics

2017 ◽  
Vol 13 (2) ◽  
pp. 406-416 ◽  
Author(s):  
Barbi Gogoi ◽  
Dhrubajyoti Gogoi ◽  
Yumnam Silla ◽  
Bibhuti Bhushan Kakoti ◽  
Brijmohan Singh Bhau
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Cancer Therapeutics ◽  
Network Pharmacology ◽  
Anticancer Compounds ◽  
Pharmacological Approach ◽  
Anti Cancer

In the present work, latest network pharmacological approach has been used for the screening of natural anticancer compounds from Clerodendrum species.

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