In silico de novo design of novel NNRTIs: a bio-molecular modelling approach

RSC Advances ◽  
2015 ◽  
Vol 5 (19) ◽  
pp. 14814-14827 ◽  
Author(s):  
Nilanjana Jain (Pancholi) ◽  
Swagata Gupta ◽  
Neelima Sapre ◽  
Nitin S. Sapre
Keyword(s):  
Interaction Potential ◽  
Molecular Modelling ◽  
In Silico ◽  
De Novo ◽  
De Novo Design ◽  
High Efficacy ◽  
Structural Requirements ◽  
Structural Descriptors ◽  
Modelling Approach

Six novel NNRTIs (DABO) with high efficacy are designed by assessing the interaction potential and structural requirements using chemometric analyses (SVM, BPNN and MLR) on structural descriptors.

Towards the de novo design of DNA based catalytic sites using a combined NMR and in silico approach

2014 ◽  
Author(s):  
Dieter Buyst ◽  
V. Gheerardijn ◽  
J. Van Den Begin ◽  
A. Madder ◽  
J. C. Martins
Keyword(s):  
In Silico ◽  
De Novo ◽  
De Novo Design ◽  
Catalytic Sites

scholarly journals de novo Design and in silico Optimization of Antibody-Like Binders Targeting Ebola Viral Antigen

2016 ◽  
Vol 110 (3) ◽  
pp. 537a
Author(s):  
Muyun Lihan ◽  
Boon Chong Goh ◽  
Tong Li ◽  
Costas D. Maranas ◽  
Klaus Shulten
Keyword(s):  
In Silico ◽  
Viral Antigen ◽  
De Novo ◽  
De Novo Design

scholarly journals Evaluation of Inhibitory Activity In Silico of In-House Thiomorpholine Compounds between the ACE2 Receptor and S1 Subunit of SARS-CoV-2 Spike

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1208
Author(s):  
Victor H. Vázquez-Valadez ◽  
Alejandro Hernández-Serda ◽  
Ma. Fernanda Jiménez-Cabiedes ◽  
Pablo Aguirre-Vidal ◽  
Ingrid González-Tapia ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
In Silico ◽  
De Novo ◽  
Computational Study ◽  
Antiviral Agents ◽  
Antihypertensive Agents ◽  
De Novo Design ◽  
Target Cells ◽  
Research Groups ◽  
International Scientific Community

At the end of 2019, the world was struck by the COVID-19 pandemic, which resulted in dire repercussions of unimaginable proportions. From the beginning, the international scientific community employed several strategies to tackle the spread of this disease. Most notably, these consisted of the development of a COVID-19 vaccine and the discovery of antiviral agents through the repositioning of already known drugs with methods such as de novo design. Previously, methylthiomorphic compounds, designed by our group as antihypertensive agents, have been shown to display an affinity with the ACE2 (angiotensin converting enzyme) receptor, a key mechanism required for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) entry into target cells. Therefore, the objective of this work consists of evaluating, in silico, the inhibitory activity of these compounds between the ACE2 receptor and the S1 subunit of the SARS-CoV-2 spike protein. Supported by the advances of different research groups on the structure of the coronavirus spike and the interaction of the latter with its receptor, ACE2, we carried out a computational study that examined the effect of in-house designed compounds on the inhibition of said interaction. Our results indicate that the polyphenol LQM322 is one of the candidates that should be considered as a possible anti-COVID-19 agent.

scholarly journals Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1

2021 ◽  
Vol 12 (14) ◽  
pp. 5164-5170
Author(s):  
Salvador Guardiola ◽  
Monica Varese ◽  
Xavier Roig ◽  
Macarena Sánchez-Navarro ◽  
Jesús García ◽  
...  
Keyword(s):  
Specific Surface ◽  
Protein Interactions ◽  
In Silico ◽  
Cyclic Peptides ◽  
De Novo ◽  
De Novo Design ◽  
Target Protein ◽  
Surface Patch ◽  
Protein Protein Interactions

In silico design of heterochiral cyclic peptides that bind to a specific surface patch on the target protein (PD-1, in this case) and disrupt protein–protein interactions.

scholarly journals Dataset on in-silico investigation on triazole derivatives via molecular modelling approach: A potential glioblastoma inhibitors

Data in Brief ◽  
2021 ◽  
Vol 34 ◽  
pp. 106703
Author(s):  
Abel Kolawole Oyebamiji ◽  
Oluwatumininu Abosede Mutiu ◽  
Folake Ayobami Amao ◽  
Olubukola Monisola Oyawoye ◽  
Temitope A Oyedepo ◽  
...  
Keyword(s):  
Molecular Modelling ◽  
In Silico ◽  
Triazole Derivatives ◽  
Modelling Approach

scholarly journals De Novo Design of Protein Kinase Inhibitors by in Silico Identification of Hinge Region-Binding Fragments

2013 ◽  
Vol 8 (5) ◽  
pp. 1044-1052 ◽  
Author(s):  
Robert Urich ◽  
Grant Wishart ◽  
Michael Kiczun ◽  
André Richters ◽  
Naomi Tidten-Luksch ◽  
...  
Keyword(s):  
Protein Kinase ◽  
In Silico ◽  
Kinase Inhibitors ◽  
De Novo ◽  
De Novo Design ◽  
Protein Kinase Inhibitors ◽  
Hinge Region ◽  
In Silico Identification

Fragment-Based Drug Design of Antitumoral Molecules Polo-like kinase 1 inhibitors: in-silico approach

2020 ◽  
Vol 18 ◽  
Author(s):  
Ayoub Attoui ◽  
Widad Sobhi ◽  
Nour El Houda Hammoudi ◽  
Yacine Benguerba
Keyword(s):  
Development Strategy ◽  
In Silico ◽  
De Novo ◽  
Pharmacophore Model ◽  
De Novo Design ◽  
Ligand Complex ◽  
Docking Simulations ◽  
Virtual Database ◽  
Promising Strategy ◽  
Therapeutic Development

Background:: Kinase enzymes are reported to be very implicated in cancer. Polo-like kinase 1 (PLK1) is a protein kinase with a marked role in tumorigenesis and its inhibition is a promising anticancer therapeutic development strategy. Objective:: The purpose of this study was de novo design of new PLK1 inhibitors using in-silico approach. Method:: A virtual compounds library based on known inhibitors was designed using BREED algorithm. Molecules were geometry optimized then filtered according to lead-like properties using QiqProp. Receptor-ligand complex-based pharmacophore model was generated with Phase and used to virtually screen the new virtual database. Glide multistage molecular docking simulations were performed for the resulted compounds followed with a Prime MM-GBSA minimization. Results:: Two compounds (prd-comp 1-2) showed acceptable binding poses with a higher docking score than known inhibitor BI2536. MM-GBSA study confirmed that the leads have better binding energy than reference ligands. All leads bind to the key amino acids Cys133, Leu59, with a focus on molecule prd-comp1, proposed to have better affinity due to direct H-bond with Asp194. Conclusion:: Modifying hydration pattern of target protein by displacing water molecule is suggested to be a promising strategy for designing new PLK1 inhibitors. This applied methodology and the retrieved hits could be useful in the design of potent inhibitors of PLK1 as antitumoral agents.

De novo design and in-silico studies of novel bis-arylpiperazine derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase

2014 ◽  
Vol 1 (2) ◽  
pp. 22
Author(s):  
Ashok Yadav ◽  
Subhash Chander ◽  
Hiren Lathiya ◽  
Hardik Sharma ◽  
Kriti Goyal ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
In Silico ◽  
De Novo ◽  
De Novo Design ◽  
In Silico Studies ◽  
Nucleoside Inhibitors ◽  
Hiv 1

scholarly journals Quest for the quenching and binding mode of functionalized ZnO QDs with calf thymus DNA: Biophysical and in silico molecular modelling approach

2022 ◽  
Vol 422 ◽  
pp. 113562
Author(s):  
Dibakar Sahoo ◽  
Abhishek Mandal ◽  
Paulami Mandal ◽  
Jyotirmayee Set
Keyword(s):  
Molecular Modelling ◽  
In Silico ◽  
Binding Mode ◽  
Calf Thymus Dna ◽  
Calf Thymus ◽  
Zno Qds ◽  
Modelling Approach
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