Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors

(2020) Clauber H. S. da Costa et al.   Journal of Chemical Information and Modeling

ON THE ASSESSMENT OF THE CRUZAIN CYSTEINE PROTEASE REVERSIBLE AND IRREVERSIBLE COVALENT INHIBITION MECHANISM

(2020) José Rogério A. Silva et al.   Journal of Chemical Information and Modeling

Exploring the Proteolysis Mechanism of the Proteasomes

(2020) Arjun Saha et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Similarities and differences between crystal and enzyme environmental effects on the electron density of drug molecules

(2020) Florian Kleemiss et al.   CHEMISTRY-A EUROPEAN JOURNAL

In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADMET screening

(2020) Adib Ghaleb et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring the concerted mechanistic pathway for HIV-1 PR—substrate revealed by umbrella sampling simulation

(2020) Zainab K. Sanusi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Synthesis, anti-bacterial evaluation, DFT study and molecular docking as a potential 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 inhibitors of a novel Schiff bases

(2020) Ahmed S.M. Al-Janabi et al.   JOURNAL OF MOLECULAR STRUCTURE

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

(2020) Kyung Eun Lee et al.   Biomolecules

Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro

(2020) Shiv Bharadwaj et al.   BRIEFINGS IN BIOINFORMATICS

Interrelated Mechanism by Which the Methide Quinone Celastrol, Obtained from the Roots of Tripterygium wilfordii, Inhibits Main Protease 3CLpro of COVID-19 and Acts as Superoxide Radical Scavenger

(2020) Francesco Caruso et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Reversed Proteolysis—Proteases as Peptide Ligases

(2020) Peter Goettig   Catalysts

Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate

(2019) Bodee Nutho et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Proteases: History, discovery, and roles in health and disease

(2019) Judith S. Bond   JOURNAL OF BIOLOGICAL CHEMISTRY

Recent advances in the development of legumain-selective chemical probes and peptide prodrugs

(2019) Marcin Poreba   BIOLOGICAL CHEMISTRY

Low susceptibility of asunaprevir towards R155K and D168A point mutations in HCV NS3/4A protease: A molecular dynamics simulation

(2019) Jirayu Kammarabutr et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Surface loops of trypsin-like serine proteases as determinants of function

(2019) Peter Goettig et al.   BIOCHIMIE

Understanding the variability of the S1′ pocket to improve matrix metalloproteinase inhibitor selectivity profiles

(2019) Aleix Gimeno et al.   DRUG DISCOVERY TODAY

Designing New Generation of Potent Inhibitors against Membrane-type Matrix Metalloproteinase-2: A Computational Effort against Multiple Myeloma

(2019) Shohreh Fakhari et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Water Plays a Cocatalytic Role in Epoxide Ring Opening Reaction in Aspartate Proteases: A QM/MM Study

(2019) Mohd Ahsan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Rebirth of Matrix Metalloproteinase Inhibitors: Moving Beyond the Dogma

(2019) Gregg B. Fields   Cells

Quantum mechanics/molecular mechanics studies of the mechanism of cysteine proteases inhibition by dipeptidyl nitroalkenes

(2019) Vicent Moliner et al.   CHEMISTRY-A EUROPEAN JOURNAL

Novel Matrix Metalloproteinase 12 Selective Radiotracers for Vascular Molecular Imaging

(2019) Jakub Toczek et al.   JOURNAL OF MEDICINAL CHEMISTRY

Natural Occurring and Engineered Enzymes for Peptide Ligation and Cyclization

(2019) Timo Nuijens et al.   Frontiers in Chemistry

Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study

(2019) Sebastián A. Cuesta et al.   MOLECULAR PHYSICS

Structure and Function of the 26S Proteasome

(2018) Jared A.M. Bard et al.   Annual Review of Biochemistry

Design, Synthesis, and Biological Evaluation of Tetrahydro-β-carboline Derivatives as Selective Sub-Nanomolar Gelatinase Inhibitors

(2018) Giuseppe Felice Mangiatordi et al.   ChemMedChem

Hybrid 2D/3D-quantitative structure–activity relationship and modeling studies perspectives of pepstatin A analogs as cathepsin D inhibitors

(2018) Olayide A Arodola et al.   Future Medicinal Chemistry

An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant

(2018) Zainab K. Sanusi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Novel mutant of Escherichia coli asparaginase II to reduction of the glutaminase activity in treatment of acute lymphocytic leukemia by molecular dynamics simulations and QM-MM studies

(2018) Noeman Ardalan et al.   MEDICAL HYPOTHESES

Matrix Metalloproteinase Inhibitors in Cancer Therapy: Turning Past Failures Into Future Successes

(2018) Arthur Winer et al.   MOLECULAR CANCER THERAPEUTICS

On the Difference Between Additive and Subtractive QM/MM Calculations

(2018) Lili Cao et al.   Frontiers in Chemistry

Screening for the selective inhibitors of MMP-9 from natural products based on pharmacophore modeling and molecular docking in combination with bioassay experiment, hybrid QM/MM calculation, and MD simulation

(2018) Jiaying Hou et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles

(2018) Alberto Monteiro Dos Santos et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors

(2018) Cyril Barinka et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling

(2018) Collins U. Ibeji et al.   TUBERCULOSIS

An n→π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole

(2018) Ian W. Windsor et al.   ACS Catalysis

Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent

(2017) Elise Duboué-Dijon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?

(2017) Payal Chatterjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

From structure to function - a family portrait of plant subtilases

(2017) Andreas Schaller et al.   NEW PHYTOLOGIST

Quantum mechanics/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones

(2017) Kemel Arafet et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Future of Cysteine Cathepsins in Disease Management

(2017) Lovro Kramer et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Distinct Roles of Catalytic Cysteine and Histidine in the Protease and Ligase Mechanisms of Human Legumain As Revealed by DFT-Based QM/MM Simulations

(2017) Brigitta Elsässer et al.   ACS Catalysis

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site

(2016) Oksana Gerlits et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure and function of legumain in health and disease

(2016) Elfriede Dall et al.   BIOCHIMIE

The life cycle of the 26S proteasome: from birth, through regulation and function and onto its death

(2016) Ido Livneh et al.   CELL RESEARCH

Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2

(2016) Tatiana Vasilevskaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations

(2016) Pooja Shrestha et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides

(2016) Yanzi Zhou et al.   Journal of Physical Chemistry Letters

Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses

(2016) Ulrich Eckhard et al.   MATRIX BIOLOGY

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain

(2016) Attila Fekete et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Reaction mechanism of the dengue virus serine protease: a QM/MM study

(2016) M. C. P. Lima et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Gates, Channels, and Switches: Elements of the Proteasome Machine

(2016) Daniel Finley et al.   TRENDS IN BIOCHEMICAL SCIENCES

Theoretical Insights into the Functioning of Metallopeptidases and Their Synthetic Analogues

(2015) Tingting Zhang et al.   ACCOUNTS OF CHEMICAL RESEARCH

Comparative structural analysis of the caspase family with other clan CD cysteine peptidases

(2015) Karen McLuskey et al.   BIOCHEMICAL JOURNAL

Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease

(2015) Shuhua Ma et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Protease signaling in animal and plant-regulated cell death

(2015) Guy S. Salvesen et al.   FEBS Journal

QM/MM Simulations of Amyloid-β 42 Degradation by IDE in the Presence and Absence of ATP

(2015) Carlos H. B. da Cruz et al.   Journal of Chemical Information and Modeling

Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

(2015) Tatiana Vasilevskaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Unravelling the reaction mechanism of matrix metalloproteinase 3 using QM/MM calculations

(2015) Gustavo Troiano Feliciano et al.   JOURNAL OF MOLECULAR STRUCTURE

Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study

(2015) Tanya Singh et al.   Molecular BioSystems

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

(2015) António J. M. Ribeiro et al.   ACS Catalysis

Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Falcipain-2 Inhibition by the Epoxysuccinate E64

(2014) Kemel Arafet et al.   BIOCHEMISTRY

Molecular insights on analogs of HIV PR inhibitors toward HTLV-1 PR through QM/MM interactions and molecular dynamics studies: comparative structure analysis of wild and mutant HTLV-1 PR

(2014) Chandrabose Selvaraj et al.   JOURNAL OF MOLECULAR RECOGNITION

Computational Characterization of Ketone–Ketal Transformations at the Active Site of Matrix Metalloproteinases

(2014) Maria G. Khrenova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases

(2014) Maria G. Khrenova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist?

(2014) José Ángel Martı́nez-González et al.   ACS Catalysis

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Reaction Pathway and Free Energy Profile for Papain-Catalyzed Hydrolysis of N-Acetyl-Phe-Gly 4-Nitroanilide

(2013) Donghui Wei et al.   BIOCHEMISTRY

Understanding the Autocatalytic Process of Pro-kumamolisin Activation from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical (QM/MM) Free-Energy Simulations

(2013) Jianzhuang Yao et al.   CHEMISTRY-A EUROPEAN JOURNAL

Validation of potential inhibitors for SrtA againstBacillus anthracisby combined approach of ligand-based and molecular dynamics simulation

(2013) Chandrabose Selvaraj et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Benchmark Study for the Cysteine–Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches

(2013) Alexander Paasche et al.   Journal of Chemical Theory and Computation

Elucidating the catalytic mechanism of β-secretase (BACE1): A quantum mechanics/molecular mechanics (QM/MM) approach

(2013) Arghya Barman et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-Principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

(2013) Donghui Wei et al.   JOURNAL OF PHYSICAL CHEMISTRY B

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2013) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Caspase Substrates and Inhibitors

(2013) M. Poreba et al.   Cold Spring Harbor Perspectives in Biology

Proteasome inhibitors mechanism; source for design of newer therapeutic agents

(2012) Sunil L Harer et al.   JOURNAL OF ANTIBIOTICS

Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors

(2012) Florent Barbault et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors

(2012) Maya M. Makatini et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Combined QM/MM (ONIOM) and QSAR Approach to the Study of Complex Formation of Matrix Metalloproteinase-9 with a Series of Biphenylsulfonamides–LERE-QSAR Analysis (V)

(2012) Tatsusada Yoshida et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fundamental Reaction Pathway and Free Energy Profile for Inhibition of Proteasome by Epoxomicin

(2012) Donghui Wei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The catalytic mechanism of mouse renin studied with QM/MM calculations

(2012) Natércia F. Brás et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An Integrated Computational Approach to Rationalize the Activity of Non-Zinc-Binding MMP-2 Inhibitors

(2012) Antonella Di Pizio et al.   PLoS One

Transition states of native and drug-resistant HIV-1 protease are the same

(2012) D. R. Kipp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cysteine cathepsins: From structure, function and regulation to new frontiers

(2011) Vito Turk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

A quantum mechanical/molecular mechanical study of the aspartic protease plasmepsin IV complexed with allophenylnorstatine-based inhibitor

(2011) Natália de Farias Silva et al.   CHEMICAL PHYSICS LETTERS

A QM/MM study of the binding of RAPTA ligands to cathepsin B

(2011) Antonella Ciancetta et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Novel 1-Hydroxypiperazine-2,6-diones as New Leads in the Inhibition of Metalloproteinases

(2011) Sérgio M. Marques et al.   JOURNAL OF MEDICINAL CHEMISTRY

Computational analysis of aspartic protease plasmepsin II complexed with EH58 inhibitor: a QM/MM MD study

(2011) Natália de Farias Silva et al.   JOURNAL OF MOLECULAR MODELING

Enhancing QM/MM Molecular Dynamics Sampling in Explicit Environments via an Orthogonal-Space-Random-Walk-Based Strategy

(2011) Donghong Min et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Catalytic Mechanism and Roles of Arg197 and Thr183 in theStaphylococcus aureusSortase A Enzyme

(2011) Bo-Xue Tian et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1

(2010) José L. Domínguez et al.   BIOCHEMISTRY

Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate

(2010) Yanzi Zhou et al.   CHEMICAL COMMUNICATIONS

Bridging quantum mechanics and structure-based drug design

(2010) Marco De Vivo   Frontiers in Bioscience-Landmark

Insights from Selective Non-phosphinic Inhibitors of MMP-12 Tailored to Fit with an S1′ Loop Canonical Conformation

(2010) Laurent Devel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue

(2010) Jia Zhou et al.   Journal of Chemical Theory and Computation

Catalysis of Carboxypeptidase A: Promoted-Water versus Nucleophilic Pathways

(2010) Shanshan Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding the Mechanism of Deacylation Reaction Catalyzed by the Serine Carboxyl Peptidase Kumamolisin-As: Insights from QM/MM Free Energy Simulations

(2010) Qin Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B

(2010) Alejandro Rodríguez et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Reaction Mechanism of Glutamate Carboxypeptidase II Revealed by Mutagenesis, X-ray Crystallography, and Computational Methods

(2009) Vojtěch Klusák et al.   BIOCHEMISTRY

Matrix Metalloproteinase 2 Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of (4-Phenoxyphenylsulfonyl)methylthiirane and Its Oxirane Analogue

(2009) Peng Tao et al.   BIOCHEMISTRY

Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease

(2009) Pedro Fong et al.   Journal of Chemical Information and Modeling

Environmental Effects on Charge Densities of Biologically Active Molecules: Do Molecule Crystal Environments Indeed Approximate Protein Surroundings?

(2009) Milena Mladenovic et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Matrix Metalloproteinase 2 (MMP2) Inhibition: DFT and QM/MM Studies of the Deprotonation-Initialized Ring-Opening Reaction of the Sulfoxide Analogue of SB-3CT

(2009) Peng Tao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations

(2009) Natalia Díaz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

(2008) Hao Hu et al.   Annual Review of Physical Chemistry

Application quantum and physico chemical molecular descriptors utilizing principal components to study mode of anticoagulant activity of pyridyl chromen-2-one derivatives

(2008) M.S. Bhatia et al.   BIOORGANIC & MEDICINAL CHEMISTRY

QM/QM studies for Michael reaction in coronavirus main protease (3CLPro)

(2008) Alex G. Taranto et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Interpretation of Protein/Ligand Crystal Structure using QM/MM Calculations: Case of HIV-1 Protease/Metallacarborane Complex

(2008) Jindřich Fanfrlík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomistic Insights into the Inhibition of Cysteine Proteases: First QM/MM Calculations Clarifying the Stereoselectivity of Epoxide-Based Inhibitors

(2008) Milena Mladenovic et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Hydrolysis Catalyzed by Matrix Metalloproteinase 2: A Computational Study

(2008) Dr. Natalia Díaz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Origin of the Stabilization of the Zwitterionic Resting State of Cysteine Proteases: A Theoretical Study

(2008) Milena Mladenovic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-ray Diffraction

(2008) Leighton Coates et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Combined QM/MM mechanistic study of the acylation process in furin complexed with the H5N1 avian influenza virus hemagglutinin's cleavage site

(2008) Thanyada Rungrotmongkol et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS