Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates

R Yoshino, N Yasuo, M Sekijima - Scientific reports, 2020 - nature.com
The number of cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
infection (COVID-19) has reached over 114,000. SARS-CoV-2 caused a pandemic in …

Traditional and Novel Computer-Aided Drug Design (CADD) Approaches in the Anticancer Drug Discovery Process

N del Carmen Quintal Bojórquez… - Current Cancer Drug …, 2023 - ingentaconnect.com
Background: In the last decade, cancer has been a leading cause of death worldwide.
Despite the impressive progress in cancer therapy, firsthand treatments are not selective to …

Improved method of structure-based virtual screening via interaction-energy-based learning

N Yasuo, M Sekijima - Journal of chemical information and …, 2019 - ACS Publications
Virtual screening is a promising method for obtaining novel hit compounds in drug
discovery. It aims to enrich potentially active compounds from a large chemical library for …

Screening for inhibitors of main protease in SARS-CoV-2: in silico and in vitro approach avoiding peptidyl secondary amides

KZ Yamamoto, N Yasuo, M Sekijima - Journal of Chemical …, 2022 - ACS Publications
In addition to vaccines, antiviral drugs are essential for suppressing COVID-19. Although
several inhibitor candidates were reported for SARS-CoV-2 main protease, most are highly …

IEV2Mol: Molecular Generative Model Considering Protein–Ligand Interaction Energy Vectors

M Ozawa, S Nakamura, N Yasuo… - Journal of Chemical …, 2024 - ACS Publications
Generating drug candidates with desired protein–ligand interactions is a significant
challenge in structure-based drug design. In this study, a new generative model, IEV2Mol, is …

[HTML][HTML] Novel Glycomimetics Protect against Glycated Low-Density Lipoprotein-Induced Vascular Calcification In Vitro via Attenuation of the RAGE/ERK/CREB …

GP Sidgwick, R Weston, AM Mahmoud, A Schiro… - Cells, 2024 - mdpi.com
Heparan sulphate (HS) can act as a co-receptor on the cell surface and alterations in this
process underpin many pathological conditions. We have previously described the …

Molecular dynamics simulation reveals the mechanism by which the influenza cap-dependent endonuclease acquires resistance against baloxavir marboxil

R Yoshino, N Yasuo, M Sekijima - Scientific reports, 2019 - nature.com
Baloxavir marboxil (BXM), an antiviral drug for influenza virus, inhibits RNA replication by
binding to RNA replication cap-dependent endonuclease (CEN) of influenza A and B …

Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance …

G Tutumlu, B Dogan, T Avsar, MD Orhan… - Frontiers in …, 2020 - frontiersin.org
Antiapoptotic members of B-cell leukemia/lymphoma-2 (BCL-2) family proteins are one of
the overexpressed proteins in cancer cells that are oncogenic targets. As such, targeting of …

Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach

N Wakui, R Yoshino, N Yasuo, M Ohue… - Journal of Molecular …, 2018 - Elsevier
Abstract B-cell lymphoma 2 (Bcl-2) family proteins are potential drug targets in cancer and
have a relatively flat and flexible binding site. ABT-199 is one of the most promising selective …

Computational approaches for identifying potential inhibitors on targeting protein interactions in drug discovery

V Kanakaveti, A Shanmugam, C Ramakrishnan… - Advances in protein …, 2020 - Elsevier
In the era of big data, the interplay of artificial and human intelligence is the demanding job
to address the concerns involving exchange of decisions between both sides. Drug …