Next generation 3D pharmacophore modeling

D Schaller, D Šribar, T Noonan, L Deng… - Wiley …, 2020 - Wiley Online Library
Abstract 3D pharmacophore models are three‐dimensional ensembles of chemically
defined interactions of a ligand in its bioactive conformation. They represent an elegant way …

Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates

J Kirchmair, S Distinto, D Schuster… - Current medicinal …, 2008 - ingentaconnect.com
Computational chemistry software for lead discovery has become well established in
pharmaceutical industry and has found its way to the desktop computers of medicinal …

Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex

PA Holt, JB Chaires, JO Trent - Journal of chemical information …, 2008 - ACS Publications
The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic
structures of a collection of small molecule ligands that have been shown to bind nucleic …

Tracking the binding site of anticancer drug fluxoridin with Fe-related proteins to achieve intelligent drug delivery

S Shahraki, HS Delarami, Z Razmara… - Spectrochimica Acta Part A …, 2024 - Elsevier
In cancer cells that need a lot of iron for growth and metastasis, halo-transferrin (TF-
containing iron) enters the cell with the help of the transferrin receptor 1 (TFR1) protein. If the …

Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies

R Sultana, A Ali, C Twala, R Mehandi… - Journal of …, 2023 - Taylor & Francis
We have synthesized the pyrazole-bearing Schiff base derivatives (5a–5e) and (6a–6h) then
the structural confirmation was supported by various spectral analyses. The antibacterial …

The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery

J Kirchmair, P Markt, S Distinto… - Journal of medicinal …, 2008 - ACS Publications
In 1970, at a time when structural information of one atom was stored on a single punched
card, the crystallographers Helen M. Berman, Edgar Meyer, and Gerson Cohen began …

Structural and functional changes of catalase through interaction with Erlotinib hydrochloride. Use of Chou's 5-steps rule to study mechanisms

S Shahraki, HS Delarami, M Poorsargol… - Spectrochimica Acta Part …, 2021 - Elsevier
Erlotinib hydrochloride (Erlo) is used in the treatment of non-small cell lung cancer,
pancreatic cancer and other types of cancer. Interaction of small molecules with bio …

Probing the combination of erlotinib hydrochloride, an anticancer drug, and human serum albumin: Spectroscopic, molecular docking, and molecular dynamic …

S Shahraki, Z Razmara, HS Delarami… - …, 2023 - Wiley Online Library
Human serum albumin (HSA) is a globular and monomeric protein in plasma that transports
many drugs and compounds. Binding of some drugs to HSA can lead to changes in its …

Investigation of kinetics and thermodynamics in the interaction process between two pyridine derived Schiff base complexes and catalase

S Shahraki, HS Delarami, H Mansouri-Torshizi… - Journal of Molecular …, 2021 - Elsevier
In the present study, two new Zn (II) complexes had been prepared by an N 2 bidentate
Schiff base ligand 4-pyridylimine-1, 2-diacetylmonoxime (PIAO)(a:[Zn (PIAO) 2] Cl 2, b:[Zn …

Molecular docking and inhibitory effects of a novel cytotoxic agent with bovine liver catalase

S Shahraki, M Saeidifar, HS Delarami… - Journal of Molecular …, 2020 - Elsevier
The synthesis of new metal complexes with fewer side effects than old drugs, such as
cisplatin, is the major research pathway of many scientists. In this regard, the study of …