Computational and In Vitro Investigation of (-)-Epicatechin and Proanthocyanidin B2 as Inhibitors of Human Matrix Metalloproteinase 1

Design and Molecular dynamic Investigations of 7,8-Dihydroxyflavone Derivatives as Potential Neuroprotective Agents Against Alpha-synuclein

(2020) Mohankumar Thangavel et al.   Scientific Reports

Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation

(2020) Shiv Bharadwaj et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Density functional theory and molecular dynamics simulation support Ganoderma lucidum triterpenoids as broad range antagonist of matrix metalloproteinases

(2020) Shiv Bharadwaj et al.   JOURNAL OF MOLECULAR LIQUIDS

N+-C-H···O Hydrogen bonds in protein-ligand complexes

(2019) Yukihiro Itoh et al.   Scientific Reports

Computational aided mechanistic understanding of Camellia sinensis bioactive compounds against co-chaperone p23 as potential anticancer agent

(2019) Shiv Bharadwaj et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Trichormamide C Structural Confirmation through Total Synthesis and Extension to Analogs

(2019) Laurine Darcel et al.   ORGANIC LETTERS

Discovery of Ganoderma lucidum triterpenoids as potential inhibitors against Dengue virus NS2B-NS3 protease

(2019) Shiv Bharadwaj et al.   Scientific Reports

Screening of a hundred plant extracts as tyrosinase and elastase inhibitors, two enzymatic targets of cosmetic interest

(2018) I. Chiocchio et al.   INDUSTRIAL CROPS AND PRODUCTS

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations

(2017) Ido Y. Ben-Shalom et al.   Journal of Chemical Information and Modeling

Triolein reduces MMP-1 upregulation in dermal fibroblasts generated by ROS production in UVB-irradiated keratinocytes

(2017) Gustavo J. Leirós et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Learning Medicinal Chemistry Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) Rules from Cross-Company Matched Molecular Pairs Analysis (MMPA)

(2017) Christian Kramer et al.   JOURNAL OF MEDICINAL CHEMISTRY

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

(2017) Antoine Daina et al.   Scientific Reports

Structure Based docking studies towards exploring potential anti-androgen activity of selected phytochemicals against Prostate Cancer

(2017) Anshika N. Singh et al.   Scientific Reports

Calculation of Configurational Entropy Differences from Conformational Ensembles Using Gaussian Mixtures

(2016) Gergely Gyimesi et al.   Journal of Chemical Theory and Computation

Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates

(2016) Simon Hikiri et al.   Journal of Chemical Theory and Computation

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy

(2016) Lili Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New multi-component solid forms of anti-cancer drug Erlotinib: role of auxiliary interactions in determining a preferred conformation

(2016) Palash Sanphui et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Extracellular Matrix and Dermal Fibroblast Function in the Healing Wound

(2016) Lauren E. Tracy et al.   Advances in Wound Care

Tiron Inhibits UVB-Induced AP-1 Binding Sites Transcriptional Activation on MMP-1 and MMP-3 Promoters by MAPK Signaling Pathway in Human Dermal Fibroblasts

(2016) Jing Lu et al.   PLoS One

Diphlorethohydroxycarmalol Suppresses Ultraviolet B-Induced Matrix Metalloproteinases via Inhibition of JNK and ERK Signaling in Human Keratinocytes

(2015) Mei Jing Piao et al.   Biomolecules & Therapeutics

The potency–insolubility conundrum in pharmaceuticals: Mechanism and solution for hepatitis C protease inhibitors

(2015) Patrick R. Connelly et al.   BIOPHYSICAL CHEMISTRY

Fibroblast heterogeneity and its implications for engineering organotypic skin models in vitro

(2015) Gopu Sriram et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Computational Prediction of Molecular Hydration Entropy with Hybrid Scaled Particle Theory and Free-Energy Perturbation Method

(2015) Hwanho Choi et al.   Journal of Chemical Theory and Computation

(−)-Epigallocatechin-3-gallate inhibits matrix metalloproteinases in oral ulcers

(2015) Bin Huang et al.   RSC Advances

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

(2015) Karel Mena-Ulecia et al.   PLoS One

Stabilization of Microtubules by Taxane Diterpenoids: Insight from Docking and MD simulations

(2014) Umesh Yadava et al.   JOURNAL OF BIOLOGICAL PHYSICS

Peroxisome proliferator-activated receptor δ modulates MMP-2 secretion and elastin expression in human dermal fibroblasts exposed to ultraviolet B radiation

(2014) Sun Ah Ham et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

(2013) Samuel Genheden et al.   Journal of Chemical Theory and Computation

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of Isoxanthopterin

(2013) N. Prabavathi et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

The influence of flavonoid compounds on the in vitro inhibition study of a human fibroblast collagenase catalytic domain expressed in E. coli

(2012) Thi Thanh Hanh Nguyen et al.   ENZYME AND MICROBIAL TECHNOLOGY

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

(2012) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

(2012) Richard Lonsdale et al.   Journal of Chemical Theory and Computation

Calculation of Molecular Entropies Using Temperature Integration

(2012) Kim Sharp   Journal of Chemical Theory and Computation

Cultivated ginseng suppresses ultraviolet B–induced collagenase activation via mitogen-activated protein kinases and nuclear factor κB/activator protein-1–dependent signaling in human dermal fibroblasts

(2012) Yong Pil Hwang et al.   NUTRITION RESEARCH

Proteomic Analysis of Aorta and Protective Effects of Grape Seed Procyanidin B2 in db/db Mice Reveal a Critical Role of Milk Fat Globule Epidermal Growth Factor-8 in Diabetic Arterial Damage

(2012) Fei Yu et al.   PLoS One

Induction of lactadherin mediates the apoptosis of endothelial cells in response to advanced glycation end products and protective effects of grape seed procyanidin B2 and resveratrol

(2011) Bao-ying Li et al.   APOPTOSIS

A comparison of crystallographic and DFT optimized geometries on two taxane diterpenoids and docking studies with phospholipase A2

(2011) Umesh Yadava et al.   MEDICINAL CHEMISTRY RESEARCH

Human matrix metalloproteinases: An ubiquitarian class of enzymes involved in several pathological processes

(2011) Diego Sbardella et al.   MOLECULAR ASPECTS OF MEDICINE

Myricetin suppresses UVB-induced wrinkle formation and MMP-9 expression by inhibiting Raf

(2010) Sung Keun Jung et al.   BIOCHEMICAL PHARMACOLOGY

Probing theα-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis

(2010) Zuojun Guo et al.   Chemical Biology & Drug Design

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

A Medicinal Chemist’s Guide to Molecular Interactions

(2010) Caterina Bissantz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Matrix-Degrading Metalloproteinases in Photoaging

(2009) Taihao Quan et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY SYMPOSIUM PROCEEDINGS

Grape Seed Extract Suppresses Lipopolysaccharide-Induced Matrix Metalloproteinase (MMP) Secretion by Macrophages and Inhibits Human MMP-1 and -9 Activities

(2009) Vu Dang La et al.   JOURNAL OF PERIODONTOLOGY

Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study

(2008) Sunil K. Panigrahi   AMINO ACIDS

Calorimetry and Thermodynamics in Drug Design

(2008) Jonathan B. Chaires   Annual Review of Biophysics

Dimeric procyanidin B2 inhibits constitutively active NF-κB in Hodgkin's lymphoma cells independently of the presence of IκB mutations

(2008) Gerardo G. Mackenzie et al.   BIOCHEMICAL PHARMACOLOGY

Do enthalpy and entropy distinguish first in class from best in class?

(2008) E FREIRE   DRUG DISCOVERY TODAY

Experimental electron density studies of non-steroidal synthetic estrogens: Diethylstilbestrol and dienestrol

(2008) Eric J. Yearley et al.   JOURNAL OF MOLECULAR STRUCTURE