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Liao W, Zhang R, Chen G, Zhu X, Wu W, Chen Z, Jiang C, Lin Z, Ma L, Yu H. Berberine synergises with ferroptosis inducer sensitizing NSCLC to ferroptosis in p53-dependent SLC7A11-GPX4 pathway. Biomed Pharmacother 2024; 176:116832. [PMID: 38850659 DOI: 10.1016/j.biopha.2024.116832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/10/2024] Open
Abstract
Berberine (BBR) is a compound derived from Chinese herbal medicine, known for its anticancer properties through multiple signaling pathways. However, whether BBR can inhibit tumor growth by participating in ferroptosis remains unconfirmed. In this study, we demonstrated that berberine synergistically inhibited NSCLC in combination with multiple ferroptosis inducers, and this combination synergistically down-regulated the mRNA and protein expression of SLC7A11, GPX4, and NRF2, resulting in ferroptosis accompanied by significant depletion of GSH, and aberrant accumulation of reactive oxygen species and malondialdehyde. In a lung cancer allograft model, the combination treatment exhibited enhanced anticancer effects compared to using either drug alone. Notably, p53 is critical in determining the ferroptosis sensitivity. We found that the combination treatment did not elicit a synergistic anticancer effect in cells with a p53 mutation or with exogenous expression of mutant p53. These findings provide insight into the mechanism by which combination induces ferroptosis and the regulatory role of p53 in this process. It may guide the development of new strategies for treating NSCLC, offering great medical potential for personal diagnosis and treatment.
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Affiliation(s)
- Weilin Liao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Ren Zhang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Geer Chen
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Xiaoyu Zhu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Weiyu Wu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Ziyu Chen
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Chenyu Jiang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Zicong Lin
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Lijuan Ma
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China
| | - Haijie Yu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao Special Administrative Region of China.
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2
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Siddiqui GA, Stebani JA, Wragg D, Koutsourelakis PS, Casini A, Gagliardi A. Application of Machine Learning Algorithms to Metadynamics for the Elucidation of the Binding Modes and Free Energy Landscape of Drug/Target Interactions: a Case Study. Chemistry 2023; 29:e202302375. [PMID: 37555841 DOI: 10.1002/chem.202302375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/10/2023]
Abstract
In the context of drug discovery, computational methods were able to accelerate the challenging process of designing and optimizing a new drug candidate. Amongst the possible atomistic simulation approaches, metadynamics (metaD) has proven very powerful. However, the choice of collective variables (CVs) is not trivial for complex systems. To automate the process of CVs identification, two different machine learning algorithms were applied in this study, namely DeepLDA and Autoencoder, to the metaD simulation of a well-researched drug/target complex, consisting in a pharmacologically relevant non-canonical DNA secondary structure (G-quadruplex) and a metallodrug acting as its stabilizer, as well as solvent molecules.
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Affiliation(s)
- Gohar Ali Siddiqui
- Professorship of Simulation of Nanosystems for Energy Conversion Department of Electrical and Computer Engineering School of Computation, Information and Technology, Technical University of Munich (TUM), Hans-Piloty-Str. 1, 85748, Garching b. München, Germany
| | - Julia A Stebani
- Chair of Medicinal and Bioinorganic Chemistry Department of Chemistry, School of Natural Sciences, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching b. München, Germany
| | - Darren Wragg
- Chair of Medicinal and Bioinorganic Chemistry Department of Chemistry, School of Natural Sciences, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching b. München, Germany
| | - Phaedon-Stelios Koutsourelakis
- Professorship for Data-driven Materials Modeling School of Engineering and Design, Technical University of Munich (TUM), Boltzmannstr. 15, 85748, Garching b. München, Germany
| | - Angela Casini
- Chair of Medicinal and Bioinorganic Chemistry Department of Chemistry, School of Natural Sciences, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching b. München, Germany
| | - Alessio Gagliardi
- Professorship of Simulation of Nanosystems for Energy Conversion Department of Electrical and Computer Engineering School of Computation, Information and Technology, Technical University of Munich (TUM), Hans-Piloty-Str. 1, 85748, Garching b. München, Germany
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3
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Baser A, Basar B, Dogan HB, Sener G, Ozsamur NG, Celik FS, Altves S, Erbas-Cakmak S. Reprograming cancer cells by a BODIPY G-quadruplex stabiliser. Chem Commun (Camb) 2023; 59:12447-12450. [PMID: 37779498 DOI: 10.1039/d3cc03453d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
A cationic BODIPY-based G-quadruplex-selective stabiliser is developed and shown to decrease cancer cell migration-invasion up to 90%. The expression of critical genes (HIF1α, VIM, CDH1) related to metastasis is modulated. The stabiliser reprograms hypoxia-adaptive metabolism and an 1.82-fold increase in O2 consumption, enabling back-to-normal switching of energy metabolism, is observed. Stabilisers with a strong G-quadruplex affinity (0.38 μM Kd) significantly contribute to small molecule anti-cancer approaches.
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Affiliation(s)
- Aminesena Baser
- Konya Food and Agriculture University, Beysehir Cd. No: 9 Meram, Konya, Turkey
| | - Beyza Basar
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Ahmet Kelesoglu Yerleskesi, Meram, 42090, Konya, Turkey.
- Science and Research Application Center (BİTAM), Necmettin Erbakan University, Koycegiz Yerleskesi, Meram, 42140, Konya, Turkey
| | - Hanim Beyza Dogan
- Konya Food and Agriculture University, Beysehir Cd. No: 9 Meram, Konya, Turkey
| | - Gulnur Sener
- Konya Food and Agriculture University, Beysehir Cd. No: 9 Meram, Konya, Turkey
| | - Nezahat Gokce Ozsamur
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Ahmet Kelesoglu Yerleskesi, Meram, 42090, Konya, Turkey.
- Science and Research Application Center (BİTAM), Necmettin Erbakan University, Koycegiz Yerleskesi, Meram, 42140, Konya, Turkey
| | - Fatma Secer Celik
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Ahmet Kelesoglu Yerleskesi, Meram, 42090, Konya, Turkey.
| | - Safaa Altves
- Department of Medicinal Biology, Institute of Health Sciences, Necmettin Erbakan University, Meram, 42080, Konya, Turkey
| | - Sundus Erbas-Cakmak
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Ahmet Kelesoglu Yerleskesi, Meram, 42090, Konya, Turkey.
- Science and Research Application Center (BİTAM), Necmettin Erbakan University, Koycegiz Yerleskesi, Meram, 42140, Konya, Turkey
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4
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Zantza I, Pyrris Y, Raniolo S, Papadaki GF, Lambrinidis G, Limongelli V, Diallinas G, Mikros E. Uracil/H + Symport by FurE Refines Aspects of the Rocking-bundle Mechanism of APC-type Transporters. J Mol Biol 2023; 435:168226. [PMID: 37544358 DOI: 10.1016/j.jmb.2023.168226] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Transporters mediate the uptake of solutes, metabolites and drugs across the cell membrane. The eukaryotic FurE nucleobase/H+ symporter of Aspergillus nidulans has been used as a model protein to address structure-function relationships in the APC transporter superfamily, members of which are characterized by the LeuT-fold and seem to operate by the so-called 'rocking-bundle' mechanism. In this study, we reveal the binding mode, translocation and release pathway of uracil/H+ by FurE using path collective variable, funnel metadynamics and rational mutational analysis. Our study reveals a stepwise, induced-fit, mechanism of ordered sequential transport of proton and uracil, which in turn suggests that FurE, functions as a multi-step gated pore, rather than employing 'rocking' of compact domains, as often proposed for APC transporters. Finally, our work supports that specific residues of the cytoplasmic N-tail are involved in substrate translocation, in line with their essentiality for FurE function.
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Affiliation(s)
- Iliana Zantza
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
| | - Yiannis Pyrris
- Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15781, Greece.
| | - Stefano Raniolo
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano 6900, Switzerland.
| | - Georgia F Papadaki
- Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15781, Greece
| | - George Lambrinidis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano 6900, Switzerland; Department of Pharmacy, University of Naples "Federico II", Naples 80131, Italy.
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15781, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion 70013, Greece.
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece; Athena Research and Innovation Center in Information Communication & Knowledge Technologies, Marousi 15125, Greece.
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5
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Motta S, Siani P, Donadoni E, Frigerio G, Bonati L, Di Valentin C. Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles. NANOSCALE 2023; 15:7909-7919. [PMID: 37066796 DOI: 10.1039/d3nr00397c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Inorganic nanoparticles show promising properties that allow them to be efficiently used as drug carriers. The main limitation in this type of application is currently the drug loading capacity, which can be overcome with a proper functionalization of the nanoparticle surface. In this study, we present, for the first time, a computational approach based on metadynamics to estimate the binding free energy of the doxorubicin drug (DOX) to a functionalized TiO2 nanoparticle under different pH conditions. On a thermodynamic basis, we demonstrate the robustness of our approach to capture the overall mechanism behind the pH-triggered release of DOX due to environmental pH changes. Notably, binding free energy estimations align well with what is expected for a pH-sensitive drug delivery system. Based on our results, we envision the use of metadynamics as a promising computational tool for the rational design and in silico optimization of organic ligands with improved drug carrier properties.
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Affiliation(s)
- Stefano Motta
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Laura Bonati
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
- BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, Italy
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6
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Zhang X, Barrow J, van Mourik T, Bühl M. Towards Computational Modeling of Ligand Binding to the ILPR G-Quadruplex. Molecules 2023; 28:molecules28083447. [PMID: 37110681 PMCID: PMC10145587 DOI: 10.3390/molecules28083447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 04/29/2023] Open
Abstract
Using a combination of unconstrained and constrained molecular dynamics simulations, we have evaluated the binding affinities between two porphyrin derivatives (TMPyP4 and TEGPy) and the G-quadruplex (G4) of a DNA fragment modeling the insulin-linked polymorphic region (ILPR). Refining a well-established potential of mean force (PMF) approach to selections of constraints based on root-mean-square fluctuations results in an excellent agreement between the calculated and observed absolute free binding energy of TMPyP4. The binding affinity of IPLR-G4 toward TEGPy is predicted to be higher than that toward TMPyP4 by 2.5 kcal/mol, which can be traced back to stabilization provided by the polyether side chains of TMPyP4 that can nestle into the grooves of the quadruplex and form hydrogen bonds through the ether oxygen atoms. Because our refined methodology can be applied to large ligands with high flexibility, the present research opens an avenue for further ligand design in this important area.
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Affiliation(s)
- Xiaotong Zhang
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - John Barrow
- School of Medicine, Medical Sciences and Nutrition, Institute of Education in Healthcare and Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Michael Bühl
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
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7
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Suganthi S, Alexander A, Pillai AS, Enoch IVMV, Yousuf S. Naphtholylimino-tether on β-cyclodextrin: Selective G-quadruplex DNA binding. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Siemons N, Pearce D, Cendra C, Yu H, Tuladhar SM, Hallani RK, Sheelamanthula R, LeCroy GS, Siemons L, White AJP, McCulloch I, Salleo A, Frost JM, Giovannitti A, Nelson J. Impact of Side-Chain Hydrophilicity on Packing, Swelling, and Ion Interactions in Oxy-Bithiophene Semiconductors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204258. [PMID: 35946142 DOI: 10.1002/adma.202204258] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid-state packing and polymer-electrolyte interactions being poorly understood. Presented here is a molecular dynamics (MD) force field for modeling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray diffraction (XRD), show that alkoxylated polythiophenes will pack with a "tilted stack" and straight interdigitating side chains, whilst their glycolated counterpart will pack with a "deflected stack" and an s-bend side-chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals-through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways triethylene glycol polymers can bind to cations are revealed, showing the formation of a metastable single bound state, or an energetically deep double bound state, both with a strong side-chain length dependence. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors.
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Affiliation(s)
- Nicholas Siemons
- Department of Physics, Imperial College, London, Exhibition Rd, South Kensington, London, SW7 2AZ, UK
| | - Drew Pearce
- Department of Physics, Imperial College, London, Exhibition Rd, South Kensington, London, SW7 2AZ, UK
| | - Camila Cendra
- Department of Materials Science and Engineering, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Hang Yu
- Department of Physics, Imperial College, London, Exhibition Rd, South Kensington, London, SW7 2AZ, UK
| | - Sachetan M Tuladhar
- Department of Physics, Imperial College, London, Exhibition Rd, South Kensington, London, SW7 2AZ, UK
| | - Rawad K Hallani
- Physical Sciences and Engineering Division, KAUST Solar Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Rajendar Sheelamanthula
- Physical Sciences and Engineering Division, KAUST Solar Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Garrett S LeCroy
- Department of Materials Science and Engineering, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Lucas Siemons
- Structural biology of cells and viruses laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andrew J P White
- Chemical Crystallography Laboratory, Department of Chemistry, Imperial College London White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Iain McCulloch
- Department of Chemistry, University of Oxford, Oxford, OX1 2JD, UK
| | - Alberto Salleo
- Department of Materials Science and Engineering, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Jarvist M Frost
- Department of Physics, Imperial College, London, Exhibition Rd, South Kensington, London, SW7 2AZ, UK
| | - Alexander Giovannitti
- Department of Materials Science and Engineering, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Jenny Nelson
- Department of Physics, Imperial College, London, Exhibition Rd, South Kensington, London, SW7 2AZ, UK
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9
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Kim H, Pak Y. Improving All-Atom Force Field to Accurately Describe DNA G-Quadruplex Loops. J Phys Chem B 2022; 126:6199-6209. [PMID: 35951994 DOI: 10.1021/acs.jpcb.2c04256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA G-quadruplex (GQ) displays structural polymorphisms, and interactions between its loops and flanking sequences critically determine which of the diverse GQ conformers is adopted. All-atom molecular dynamics (MD) simulations of GQs are computationally challenging due to slow folding times and force field (ff) artifacts. In an earlier study, a direct folding simulation of the simplest DNA GQ (TBA15) was first reported using a modified version of the AMBER bsc1 ff (bsc1_vdW ff). Despite this successful folding simulation, it was later found that the bsc1_vdW ff is somewhat limited in terms of describing loop structures of GQs, which is problematic because GQ loop regions play key roles in ligand binding to modulate GQ activities. In this study, we further modified the bsc1_vdW ff to enhance the GQ loop prediction by fine-tuning a limited number of van der Waals (vdW) parameters of the standard AMBER bsc1 ff to improve the GQ loop distribution of a target GQ system (three-layered antiparallel GQ; mHtel21). Test simulations of this newly generated ff (bsc1_vdWL ff) on DNA GQs with diverse topologies (hybrid1, hybrid2, and parallel propeller) revealed that loop structures were predicted more accurately than by the bsc1_vdW ff. We consider that enhanced sampling MD simulation methods in combination with bsc1_vdWL provide useful simulation protocols for resolving outstanding issues of DNA GQ folding and GQ/ligand binding at the all-atom level.
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Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, S. Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, S. Korea
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10
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Clovis NS, Sen S. G-Tetrad-Selective Ligand Binding Kinetics in G-Quadruplex DNA Probed with Fluorescence Correlation Spectroscopy. J Phys Chem B 2022; 126:6007-6015. [PMID: 35939531 DOI: 10.1021/acs.jpcb.2c04181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Probing the kinetics of ligand binding to biomolecules is of paramount interest in biology and pharmacology. Measurements of such kinetic processes provide information on the rate-determining steps that control the binding affinity of ligands to biomolecules, thereby predicting the mechanism of the molecular interaction. In this context, ligand binding to G-quadruplex DNA (GqDNA) structures has attracted tremendous attention primarily because of their use in possible anticancer therapy. Although a large number of G-quadruplex-specific ligands have been proposed, probing the kinetics of G-tetrad-selective binding of (multiple) ligands within a G-quadruplex DNA (GqDNA) structure remains challenging. Most of the earlier studies focused on the thermodynamics of ligand binding; however, the kinetics of ligand association and dissociation with GqDNA, particularly binding of multiple ligands within a GqDNA structure, have not been explored. Here, we propose a simple fluorescence correlation spectroscopy-based method that measures the G-tetrad-selective association and dissociation rates of ligands within a GqDNA structure by correlating the fluorescence fluctuations of a site-specific (5' or 3' end-labeled) fluorophore (Cy3) in GqDNA due to quenching of Cy3 fluorescence, induced by the ligand binding to the G-tetrads. We show that well-known GqDNA ligands, BRACO19, TMPyP4, Hoechst 33258, and Hoechst 33342, have G-tetrad-selective association and dissociation rates, which suggest site-dependent variation of free energy barriers for binding/unbinding of the ligands with GqDNA. We also show that the measured kinetic rates depend not only on the G-tetrad site (5' vs 3' end) but also on the ligand and GqDNA structures.
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Affiliation(s)
- Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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11
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Bálint M, Zsidó BZ, van der Spoel D, Hetényi C. Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design. Int J Mol Sci 2022; 23:ijms23137313. [PMID: 35806314 PMCID: PMC9267029 DOI: 10.3390/ijms23137313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
The human genome codes only a few thousand druggable proteins, mainly receptors and enzymes. While this pool of available drug targets is limited, there is an untapped potential for discovering new drug-binding mechanisms and modes. For example, enzymes with long binding cavities offer numerous prerequisite binding sites that may be visited by an inhibitor during migration from a bulk solution to the destination site. Drug design can use these prerequisite sites as new structural targets. However, identifying these ephemeral sites is challenging. Here, we introduce a new method called NetBinder for the systematic identification and classification of prerequisite binding sites at atomic resolution. NetBinder is based on atomistic simulations of the full inhibitor binding process and provides a networking framework on which to select the most important binding modes and uncover the entire binding mechanism, including previously undiscovered events. NetBinder was validated by a study of the binding mechanism of blebbistatin (a potent inhibitor) to myosin 2 (a promising target for cancer chemotherapy). Myosin 2 is a good test enzyme because, like other potential targets, it has a long internal binding cavity that provides blebbistatin with numerous potential prerequisite binding sites. The mechanism proposed by NetBinder of myosin 2 structural changes during blebbistatin binding shows excellent agreement with experimentally determined binding sites and structural changes. While NetBinder was tested on myosin 2, it may easily be adopted to other proteins with long internal cavities, such as G-protein-coupled receptors or ion channels, the most popular current drug targets. NetBinder provides a new paradigm for drug design by a network-based elucidation of binding mechanisms at an atomic resolution.
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Affiliation(s)
- Mónika Bálint
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden;
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
- Correspondence:
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12
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Growth Inhibition of Two Prenylated Chalcones on Prostate Cancer Cells through the Regulation of the Biological Activity and Protein Translation of Bloom Helicase. Catalysts 2022. [DOI: 10.3390/catal12060582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Bloom (BLM) helicase is an important member of the RecQ family of DNA helicases that plays a vital role in the maintenance of genomic stability. The defect of BLM helicase leads to a human genetic disorder called Bloom syndrome, characterized by genomic instability, specific phenotypic features, and a predisposition to many types of cancer. The predisposition to cancer caused by BLM helicase is due to defects in important DNA metabolic pathways such as replication, recombination, and repair. Therefore, the aim of this work was to investigate the effects of two prenylated chalcones, WZH-10 and WZH-43, on the expression of BLM helicase in prostate cancer cells, as well as the biological activity of the purified BLM helicase from cancer cells. This might lead to a better understanding of the role of BLM helicase in the aforementioned DNA metabolic pathways that directly influence chromosomal integrity leading to cancer. The results indicated that the two prenylated chalcones inhibited the growth of prostate cancer cells PC3 by inducing apoptosis and arresting the cell cycle. However, they only inhibited the protein expression of BLM helicase without regulating its transcriptional expression. In addition, they did not significantly regulate the expression of the homologous family members WRN and RECQL1, although the DNA unwinding and ATPase activity of BLM helicase were inhibited by the two prenylated chalcones. Finally, a negligible effect was found on the DNA-binding activity of this enzyme. These results demonstrated that prenylated chalcones can be an effective intervention on the expression and function of the BLM helicase protein in cancer cells to inhibit their growth. Therefore, they might provide a novel strategy for developing new anti-cancer drugs targeting the genomic stability and DNA helicase.
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13
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Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex. Int J Mol Sci 2022; 23:ijms23105690. [PMID: 35628500 PMCID: PMC9145931 DOI: 10.3390/ijms23105690] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Previous studies suggest that berberine, an isoquinoline alkaloid, has antiviral potential and is a possible therapeutic candidate against SARS-CoV-2. The molecular underpinnings of its action are still unknown. Potential targets include quadruplexes (G4Q) in the viral genome as they play a key role in modulating the biological activity of viruses. While several DNA-G4Q structures and their binding properties have been elucidated, RNA-G4Qs such as RG-1 of the N-gene of SARS-CoV-2 are less explored. Using biophysical techniques, the berberine binding thermodynamics and the associated conformational and hydration changes of RG-1 could be characterized and compared with human telomeric DNA-G4Q 22AG. Berberine can interact with both quadruplexes. Substantial changes were observed in the interaction of berberine with 22AG and RG-1, which adopt different topologies that can also change upon ligand binding. The strength of interaction and the thermodynamic signatures were found to dependent not only on the initial conformation of the quadruplex, but also on the type of salt present in solution. Since berberine has shown promise as a G-quadruplex stabilizer that can modulate viral gene expression, this study may also contribute to the development of optimized ligands that can discriminate between binding to DNA and RNA G-quadruplexes.
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14
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Sun Z, He Q. Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels. Phys Chem Chem Phys 2022; 24:8800-8819. [PMID: 35352744 DOI: 10.1039/d2cp00355d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. Normally, due to the significant differences between the computational cost of ab initio quantum mechanics (QM) calculations and those of semi-empirical quantum mechanics (SQM) and molecular mechanics (MM), this indirect method could be used to obtain the QM thermodynamics by combining the SQM or MM results and the SQM-to-QM or MM-to-QM corrections. In our previous work, a multi-dimensional nonequilibrium pulling framework for Hamiltonian variations was introduced based on bidirectional pulling and bidirectional reweighting. The method performs nonequilibrium free energy simulations in the configurational space to obtain the thermodynamic profile along the conformational change pathway under a selected computationally efficient Hamiltonian, and uses the nonequilibrium alchemical method to correct or perturb the thermodynamic profile to that under the target Hamiltonian. The BAR-based method is designed to achieve the best generality and transferability and thus leads to modest (∼20 fold) speedup. In this work, we explore the possibility of further accelerating the nonequilibrium free energy simulation by employing unidirectional pulling and using the selection criterion to obtain the initial configurations used to initiate nonequilibrium trajectories following the idea of adaptive steered molecular dynamics (ASMD). A single initial condition is used to seed the whole multi-dimensional nonequilibrium free energy simulation and the sampling is performed fully in the nonequilibrium ensemble. Introducing very short ps-length equilibrium sampling to grab more initial seeds could also be helpful. The ASMD scheme estimates the free energy difference with the unidirectional exponential average (EXP), but it does not follow exactly the requirements of the EXP estimator. Another deficiency of the seeding simulation is the inherently sequential or serial pulling due to the inter-segment dependency, which triggers some problems in the parallelizability of the simulation. Numerical tests are performed to grasp some insights and guidelines for using this selection-criterion-based ASMD scheme. The presented selection-criterion-based multi-dimensional ASMD scheme follows the same perturbation network of the BAR-based method, and thus could be used in various Hamiltonian-variation cases.
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Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing 100871, China.
| | - Qiaole He
- AI Department of Enzymaster (Ningbo) Bio-Engineering Co., Ltd, North Century Avenue 333, 315100 Ningbo, China
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15
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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16
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Haldar S, Zhang Y, Xia Y, Islam B, Liu S, Gervasio FL, Mulholland AJ, Waller ZAE, Wei D, Haider S. Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex. J Am Chem Soc 2022; 144:935-950. [PMID: 34989224 DOI: 10.1021/jacs.1c11248] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cationic porphyrin TMPyP4 is a well-established DNA G-quadruplex (G4) binding ligand that can stabilize different topologies via multiple binding modes. However, TMPyP4 can have both a stabilizing and destabilizing effect on RNA G4 structures. The structural mechanisms that mediate RNA G4 unfolding remain unknown. Here, we report on the TMPyP4-induced RNA G4 unfolding mechanism studied by well-tempered metadynamics (WT-MetaD) with supporting biophysical experiments. The simulations predict a two-state mechanism of TMPyP4 interaction via a groove-bound and a top-face-bound conformation. The dynamics of TMPyP4 stacking on the top tetrad disrupts Hoogsteen H-bonds between guanine bases, resulting in the consecutive TMPyP4 intercalation from top-to-bottom G-tetrads. The results reveal a striking correlation between computational and experimental approaches and validate WT-MetaD simulations as a powerful tool for studying RNA G4-ligand interactions.
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Affiliation(s)
- Susanta Haldar
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K
- D.E. Shaw India Private Ltd., Hyderabad, Telangana 500096, India
| | - Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, College of Vetrinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Xia
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
| | - Barira Islam
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, U.K
| | - Sisi Liu
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Francesco L Gervasio
- Department of Chemistry, University College London, London, WC1H 0AJ, U.K
- Pharmaceutical Sciences, University of Geneva, Geneva CH-1211, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), Geneva CH-1211, Switzerland
| | | | - Zoë A E Waller
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Vetrinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, U.K
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17
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Fiorillo B, Sepe V, Conflitti P, Roselli R, Biagioli M, Marchianò S, De Luca P, Baronissi G, Rapacciuolo P, Cassiano C, Catalanotti B, Zampella A, Limongelli V, Fiorucci S. Structural Basis for Developing Multitarget Compounds Acting on Cysteinyl Leukotriene Receptor 1 and G-Protein-Coupled Bile Acid Receptor 1. J Med Chem 2021; 64:16512-16529. [PMID: 34767347 DOI: 10.1021/acs.jmedchem.1c01078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the molecular target of 40% of marketed drugs and the most investigated structures to develop novel therapeutics. Different members of the GPCRs superfamily can modulate the same cellular process acting on diverse pathways, thus representing an attractive opportunity to achieve multitarget drugs with synergic pharmacological effects. Here, we present a series of compounds with dual activity toward cysteinyl leukotriene receptor 1 (CysLT1R) and G-protein-coupled bile acid receptor 1 (GPBAR1). They are derivatives of REV5901─the first reported dual compound─with therapeutic potential in the treatment of colitis and other inflammatory processes. We report the binding mode of the most active compounds in the two GPCRs, revealing unprecedented structural basis for future drug design studies, including the presence of a polar group opportunely spaced from an aromatic ring in the ligand to interact with Arg792.60 of CysLT1R and achieve dual activity.
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Affiliation(s)
- Bianca Fiorillo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Valentina Sepe
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Paolo Conflitti
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Rosalinda Roselli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Michele Biagioli
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi 1, 06132 Perugia, Italy
| | - Silvia Marchianò
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi 1, 06132 Perugia, Italy
| | - Pasquale De Luca
- Head─Sequencing and Molecular Analyses Center, RIMAR Stazione Zoologica, Villa Comunale, 80121 Naples, Italy
| | - Giuliana Baronissi
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Pasquale Rapacciuolo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Bruno Catalanotti
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Angela Zampella
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy.,Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Stefano Fiorucci
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi 1, 06132 Perugia, Italy
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19
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Jarošová P, Hannig P, Kolková K, Mazzini S, Táborská E, Gargallo R, Borgonovo G, Artali R, Táborský P. Alkaloid Escholidine and Its Interaction with DNA Structures. BIOLOGY 2021; 10:1225. [PMID: 34943140 PMCID: PMC8698932 DOI: 10.3390/biology10121225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022]
Abstract
Berberine, the most known quaternary protoberberine alkaloid (QPA), has been reported to inhibit the SIK3 protein connected with breast cancer. Berberine also appears to reduce the bcl-2 and XIAP expression-proteins responsible for the inhibition of apoptosis. As some problems in the therapy with berberine arose, we studied the DNA binding properties of escholidine, another QPA alkaloid. CD, fluorescence, and NMR examined models of i-motif and G-quadruplex sequences present in the n-myc gene and the c-kit gene. We provide evidence that escholidine does not induce stabilization of the i-motif sequences, while the interaction with G-quadruplex structures appears to be more significant.
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Affiliation(s)
- Petra Jarošová
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Pavel Hannig
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Kateřina Kolková
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.B.)
| | - Eva Táborská
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, E-08028 Barcelona, Spain;
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.B.)
| | | | - Petr Táborský
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
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20
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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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21
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Dickerhoff J, Brundridge N, McLuckey SA, Yang D. Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution. J Med Chem 2021; 64:16205-16212. [PMID: 34677968 PMCID: PMC8614230 DOI: 10.1021/acs.jmedchem.1c01508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The medicinal natural product berberine is one of the most actively studied and pursued G-quadruplex (G4)-ligands. The major G-quadruplex formed in the promoter region of the MYC oncogene (MycG4) is an attractive drug target and a prominent example and model structure for parallel G-quadruplexes. G4-targeted berberine derivatives have been actively developed; however, the analogue design was based on a previous crystal structure in which berberine binds as a dimer to a parallel G-quadruplex. Herein, we show that in solution, the binding mode and stoichiometry of berberine are substantially different from the crystal structure: berberine binds as a monomer to MycG4 using a base-recruitment mechanism with a reversed orientation in that the positively charged convex side is actually positioned above the tetrad center. Our structure provides a physiologically relevant basis for the future structure-based rational design of G4-targeted berberine derivatives, and this study demonstrates that it is crucial to validate the ligand-DNA interactions.
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Affiliation(s)
- Jonathan Dickerhoff
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Nicole Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Danzhou Yang
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, and Purdue Institute for Drug Discovery, West Lafayette, Indiana 47907, United States
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22
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Sarkar S, Singh PC. The combined action of cations and anions of ionic liquids modulates the formation and stability of G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:24497-24504. [PMID: 34700329 DOI: 10.1039/d1cp03730g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
G-Quadruplex (Gq) formation and stabilization by any molecule is an essential requirement for its application in therapy, especially in oncology. Metal cations have shown higher propensity of the formation of the Gq structure and its stabilization. In this study, the role of both cations and anions of ionic liquids (ILs) on the Gq formation of human telomere (hTeloG) and its stability was investigated using spectroscopic and molecular dynamics simulation techniques. Irrespective of the nature of anions of ILs, tetramethylguanidinium (TMG) cations associated with different anions can form an antiparallel Gq structure in hTeloG. However, the propensity of the formation of an antiparallel Gq structure and its stability depend on the chain length of anions of ILs. Gq is significantly less stable in ILs having longer hydrocarbon chain anions compared to the short chain anions suggesting that the hydrophobicity of the anion plays a critical role in the stability and formation of the Gq structure by ILs. The data indicate that longer hydrocarbon chain anions of ILs preferably interact in the loop region of Gq through hydrophobic interaction which enhances the overall binding of the cation of ILs with Gq causing a decrease in the stacking energy between the G-quartets as well as Hoogsteen hydrogen bonds between the guanine bases leading to the destabilization of the antiparallel Gq structure.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India, 700032.
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India, 700032.
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23
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Peris-Díaz M, Guran R, Domene C, de los Rios V, Zitka O, Adam V, Krężel A. An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species. J Am Chem Soc 2021; 143:16486-16501. [PMID: 34477370 PMCID: PMC8517974 DOI: 10.1021/jacs.1c05495] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 12/16/2022]
Abstract
Mammalian metallothioneins (MTs) are a group of cysteine-rich proteins that bind metal ions in two α- and β-domains and represent a major cellular Zn(II)/Cu(I) buffering system in the cell. At cellular free Zn(II) concentrations (10-11-10-9 M), MTs do not exist in fully loaded forms with seven Zn(II)-bound ions (Zn7MTs). Instead, MTs exist as partially metal-depleted species (Zn4-6MT) because their Zn(II) binding affinities are on the nano- to picomolar range comparable to the concentrations of cellular Zn(II). The mode of action of MTs remains poorly understood, and thus, the aim of this study is to characterize the mechanism of Zn(II) (un)binding to MTs, the thermodynamic properties of the Zn1-6MT2 species, and their mechanostability properties. To this end, native mass spectrometry (MS) and label-free quantitative bottom-up and top-down MS in combination with steered molecular dynamics simulations, well-tempered metadynamics (WT-MetaD), and parallel-bias WT-MetaD (amounting to 3.5 μs) were integrated to unravel the chemical coordination of Zn(II) in all Zn1-6MT2 species and to explain the differences in binding affinities of Zn(II) ions to MTs. Differences are found to be the result of the degree of water participation in MT (un)folding and the hyper-reactive character of Cys21 and Cys29 residues. The thermodynamics properties of Zn(II) (un)binding to MT2 are found to differ from those of Cd(II), justifying their distinctive roles. The potential of this integrated strategy in the investigation of numerous unexplored metalloproteins is attested by the results highlighted in the present study.
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Affiliation(s)
- Manuel
David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Roman Guran
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Carmen Domene
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Vivian de los Rios
- Functional
Proteomics, Department of Cellular and Molecular Medicine and Proteomic
Facility, Centro de Investigaciones Biológicas
(CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ondrej Zitka
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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24
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Wang KB, Dickerhoff J, Yang D. Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-β Promoter. J Am Chem Soc 2021; 143:16549-16555. [PMID: 34586799 DOI: 10.1021/jacs.1c06200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The G-quadruplexes (G4s) formed in the PDGFR-β gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-β gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-β vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-β vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-β vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.
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25
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Ribaudo G, Ongaro A, Oselladore E, Memo M, Gianoncelli A. Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery. J Med Chem 2021; 64:13174-13190. [PMID: 34510895 PMCID: PMC8474113 DOI: 10.1021/acs.jmedchem.1c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Guanine-rich sequences
forming G-quadruplexes (GQs) are present
in several genomes, ranging from viral to human. Given their peculiar
localization, the induction of GQ formation or GQ stabilization with
small molecules represents a strategy for interfering with crucial
biological functions. Investigating the recognition event at the molecular
level, with the aim of fully understanding the triggered pharmacological
effects, is challenging. Native electrospray ionization mass spectrometry
(ESI-MS) is being optimized to study these noncovalent assemblies.
Quantitative parameters retrieved from ESI-MS studies, such as binding
affinity, the equilibrium binding constant, and sequence selectivity,
will be overviewed. Computational experiments supporting the ESI-MS
investigation and boosting its efficiency in the search for GQ ligands
will also be discussed with practical examples. The combination of
ESI-MS and in silico techniques in a hybrid high-throughput-screening
workflow represents a valuable tool for the medicinal chemist, providing
data on the quantitative and structural aspects of ligand–GQ
interactions.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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26
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Chen H, Zhou R, Pang J, Guo Y, Chen J, Kang Y, Duan M, Hou T. Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. J Chem Inf Model 2021; 62:5233-5245. [PMID: 34506144 DOI: 10.1021/acs.jcim.1c00150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
As a major drug target for anti-inflammatory therapy, the glucocorticoid receptor (GR) regulates a wide range of physiological processes through transactivation (TA) or transrepression. GR TA is involved in many adverse effects of GR-targeting drugs, and therefore, the discovery of novel GR ligands with lower TA activity and longer residence time is quite urgent. Undoubtedly, understanding the ligand dissociation mechanisms and the structural basis of the TA regulation is crucial for the development of novel GR-targeting drugs. Here, we used random accelerated molecular dynamics (RAMD) and funnel metadynamics (FM) simulations to explore the dissociation mechanisms of 5 classic glucocorticoids and 6 nonsteroidal GR ligands. Multiple ligand dissociation pathways were discovered. The classic glucocorticoids exhibit a strong preference for Path I, and most nonsteroidal ligands tend to dissociate along mixed pathways. We also find that the distinct unbinding preferences for AZD2906 and AZD9567, two representative nonsteroidal ligands with similar scaffolds but different TA activities, are primarily determined by their different polar interactions with the surrounding residues. Notably, the binding of AZD9567 poses a substantial impact on the conformation of the GR homodimer interface, which provides a valuable clue to understand the mechanisms of the TA-related side effects induced by the adjustments of the homodimerization process. These findings are critical for the structure-based rational design of novel GR ligands with more potent anti-inflammatory potency and reduced side effects.
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Affiliation(s)
- Haiyi Chen
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China.,National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Jinping Pang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Yue Guo
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Jiawen Chen
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
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27
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Sun Z, Liu Z. BAR‐Based Multi‐Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
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28
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Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota SS, Zhao J, Douglas JT, Gao P, Holmstrom ED, Miao Y, Wang J. Recognition of single-stranded nucleic acids by small-molecule splicing modulators. Nucleic Acids Res 2021; 49:7870-7883. [PMID: 34283224 PMCID: PMC8373063 DOI: 10.1093/nar/gkab602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Risdiplam is the first approved small-molecule splicing modulator for the treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 of the SMN2 pre-mRNA: (i) the 5'-splice site and (ii) an upstream purine (GA)-rich binding site. Importantly, the sequence of this GA-rich binding site significantly enhanced the potency of risdiplam analogues. In this report, we unambiguously determined that a known risdiplam analogue, SMN-C2, binds to single-stranded GA-rich RNA in a sequence-specific manner. The minimum required binding sequence for SMN-C2 was identified as GAAGGAAGG. We performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which captured spontaneous binding of a risdiplam analogue to the target nucleic acids. We uncovered, for the first time, a ligand-binding pocket formed by two sequential GAAG loop-like structures. The simulation findings were highly consistent with experimental data obtained from saturation transfer difference (STD) NMR and structure-affinity-relationship studies of the risdiplam analogues. Together, these studies illuminate us to understand the molecular basis of single-stranded purine-rich RNA recognition by small-molecule splicing modulators with an unprecedented binding mode.
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Affiliation(s)
- Zhichao Tang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Ankita Ramprasad
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Xiao Wang
- Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Sadikshya Aryal
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Srinivas S Thota
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Justin T Douglas
- Nuclear Magnetic Resonance Lab, University of Kansas, Lawrence, KS 66045, USA
| | - Philip Gao
- Protein Production Group, University of Kansas, Lawrence, KS 66047, USA
| | - Erik D Holmstrom
- Department of Molecular Biosciences and Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
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29
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Ryu HC, Windisch M, Lim JW, Choi I, Lee EK, Yoo HH, Kim TK. Thiophen urea derivatives as a new class of hepatitis C virus entry inhibitors. J Enzyme Inhib Med Chem 2021; 36:462-468. [PMID: 33455472 PMCID: PMC7822064 DOI: 10.1080/14756366.2020.1870456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
To develop unique small-molecule inhibitors of hepatitis C virus (HCV), thiophen urea (TU) derivatives were synthesised and screened for HCV entry inhibitory activities. Among them, seven TU compounds exhibited portent anti-viral activities against genotypes 1/2 (EC50 < 30 nM) and subsequently, they were further investigated; based on the pharmacological, metabolic, pharmacokinetic, and safety profiles, J2H-1701 was selected as the optimised lead compound as an HCV entry inhibitor. J2H-1701 possesses effective multi-genotypic antiviral activity. The docking results suggested the potential interaction of J2H-1701 with the HCV E2 glycoprotein. These results suggest that J2H-1701 can be a potential candidate drug for the development of HCV entry inhibitors.
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Affiliation(s)
- Hyung Chul Ryu
- R&D Center, J2H Biotech, Suwon, Gyeonggi-do, Republic of Korea
| | - Marc Windisch
- Medicinal Chemistry, Institut Pasteur Korea, Seongnam, Gyeonggi-do, Republic of Korea
| | - Jee Woong Lim
- R&D Center, J2H Biotech, Suwon, Gyeonggi-do, Republic of Korea
| | - Inhee Choi
- Medicinal Chemistry, Institut Pasteur Korea, Seongnam, Gyeonggi-do, Republic of Korea
| | - Eun Kyu Lee
- Institute of Pharmaceutical Science and Technology and College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
| | - Hye Hyun Yoo
- Institute of Pharmaceutical Science and Technology and College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
| | - Tae Kon Kim
- College of Science and Engineering, Jungwon University, Geosan-gun, Chungbuk, Republic of Korea
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30
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Banerjee N, Panda S, Chatterjee S. Frontiers in G-Quadruplex Therapeutics in Cancer: Selection of Small Molecules, Peptides and Aptamers. Chem Biol Drug Des 2021; 99:1-31. [PMID: 34148284 DOI: 10.1111/cbdd.13910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
G-quadruplex, a unique secondary structure in nucleic acids found throughout human genome, elicited widespread interest in the field of therapeutic research. Being present in key regulatory regions of oncogenes, RNAs and telomere, G-quadruplex structure regulates transcription, translation, splicing etc. Changes in its structure and stability leads to differential expression of oncogenes causing cancer. Thus, targeting G-Quadruplex structures with small molecules/other biologics has shown elevated research interest. Covering previous reports, in this review we try to enlighten the facts on the structural diversity in G-quadruplex ligands aiming to provide newer insights to design first-in-class drugs for the next generation cancer treatment.
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Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Suman Panda
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
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31
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de Felice A, Aureli S, Limongelli V. Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach. Front Mol Biosci 2021; 8:673053. [PMID: 34026848 PMCID: PMC8138314 DOI: 10.3389/fmolb.2021.673053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest human membrane receptor family regulating a wide range of cell signaling. For this reason, GPCRs are highly desirable drug targets, with approximately 40% of prescribed medicines targeting a member of this receptor family. The structural homology of GPCRs and the broad spectrum of applications of GPCR-acting drugs suggest an investigation of the cross-activity of a drug toward different GPCR receptors with the aim of rationalizing drug side effects, designing more selective and less toxic compounds, and possibly proposing off-label therapeutic applications. Herein, we present an original in silico approach named “Computational Profiling for GPCRs” (CPG), which is able to represent, in a one-dimensional (1D) string, the physico-chemical properties of a ligand–GPCR binding interaction and, through a tailored alignment algorithm, repurpose the ligand for a different GPCR. We show three case studies where docking calculations and pharmacological data confirm the drug repurposing findings obtained through CPG on 5-hydroxytryptamine receptor 2B, beta-2 adrenergic receptor, and M2 muscarinic acetylcholine receptor. The CPG code is released as a user-friendly graphical user interface with numerous options that make CPG a powerful tool to assist the drug design of GPCR ligands.
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Affiliation(s)
- Alessandra de Felice
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Simone Aureli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano, Switzerland.,Department of Pharmacy, University of Naples "Federico II", Naples, Italy
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32
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Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation. Sci Rep 2021; 11:9714. [PMID: 33958702 PMCID: PMC8102477 DOI: 10.1038/s41598-021-89215-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. The magnitudes of the binding volumes are a hallmark of packing defects and hydrational changes upon ligand binding. The conformational substates of the GQ as well as the binding strength and the stoichiometry of complex formation depend strongly on the solution conditions as well as on pressure. High hydrostatic pressure can also impact GQs inside living cells and thus affect expression of genetic information in deep sea organisms. We show that sub-kbar pressures do not only affect the conformational dynamics and structures of GQs, but also their ligand binding reactions.
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33
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Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
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Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
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34
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Aznauryan M, Noer SL, Pedersen CW, Mergny JL, Teulade-Fichou MP, Birkedal V. Ligand Binding to Dynamically Populated G-Quadruplex DNA. Chembiochem 2021; 22:1811-1817. [PMID: 33450114 DOI: 10.1002/cbic.202000792] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/11/2021] [Indexed: 12/14/2022]
Abstract
Several small-molecule ligands specifically bind and stabilize G-quadruplex (G4) nucleic acid structures, which are considered to be promising therapeutic targets. G4s are polymorphic structures of varying stability, and their formation is dynamic. Here, we investigate the mechanisms of ligand binding to dynamically populated human telomere G4 DNA by using the bisquinolinium based ligand Phen-DC3 and a combination of single-molecule FRET microscopy, ensemble FRET and CD spectroscopies. Different cations are used to tune G4 polymorphism and folding dynamics. We find that ligand binding occurs to pre-folded G4 structures and that Phen-DC3 also induces G4 formation in unfolded single strands. Following ligand binding to dynamically populated G4s, the DNA undergoes pronounced conformational redistributions that do not involve direct ligand-induced G4 conformational interconversion. On the contrary, the redistribution is driven by ligand-induced G4 folding and trapping of dynamically populated short-lived conformation states. Thus, ligand-induced stabilization does not necessarily require the initial presence of stably folded G4s.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.,Present address: Univ. Bordeaux, INSERM, CNRS ARNA, U1212, UMR 5320, IECB, 33600, Pessac, France
| | - Sofie Louise Noer
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Camilla W Pedersen
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), CNRS UMR7645, INSERM U1182, Ecole Polytechnique, 91128, Palaiseau Cedex, France.,Institute of Biophysics of the CAS, 61265, Brno, Czech Republic
| | - Marie-Paule Teulade-Fichou
- CMBC Laboratory (Chemistry and Modelling for the Biology of Cancer), Institut Curie, Research Center Orsay, CNRS UMR9187, INSERM U1196, Paris-Saclay University, Bât. 110, 91405, Orsay, France
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
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35
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Wakchaure PD, Ganguly B. Molecular level insights into the inhibition of gene expression by thiamine pyrophosphate (TPP) analogs for TPP riboswitch: A well-tempered metadynamics simulations study. J Mol Graph Model 2021; 104:107849. [PMID: 33545607 DOI: 10.1016/j.jmgm.2021.107849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Riboswitches are metabolite sensing aptamer domains present in non-coding regions in RNA and act as gene-regulating elements. Thiamine pyrophosphate (TPP) riboswitch is evolved as a new target for developing antibiotics against many pathogenic bacteria. The earlier reports suggest that the modification of the pyrophosphate group in the ligand molecule can enhance gene expression. In this work, we have examined the binding affinity and efficacy of TPP and two recently reported ligands, CH2-TPP, and CF2-TPP, using Well-tempered metadynamics (WT-MtD) simulations. The experimental in vitro assays show that both TPP and CH2-TPP repress the gene expression to the same extent. The calculated binding energies correlate well with the experimental study and show the same trend of binding affinity of ligands for the TPP riboswitch. The root mean square fluctuation profiles suggest that the CH2-TPP and TPP trigger higher fluctuations in P1 and L3 region, and such fluctuations in the P1 region is involved in the gene regulation process. The metal ion mediated contact of TPP ligand with pyrophosphate binding helix is found to be critical in the gene regulation process. The simulation results corroborate the experimental observations that the role of conformational changes occurring in different riboswitch regions upon ligand binding is essential to repress the gene expression process. This work sheds light on the subtle change in the ligand structure that can induce a more considerable impact on binding affinity and efficacy of ligands with riboswitch.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, Gujarat, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, Gujarat, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India.
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36
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Romeo I, Mesiti F, Lupia A, Alcaro S. Current Updates on Naturally Occurring Compounds Recognizing SARS-CoV-2 Druggable Targets. Molecules 2021; 26:632. [PMID: 33530467 PMCID: PMC7865633 DOI: 10.3390/molecules26030632] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified in China as the etiologic agent of the recent COVID-19 pandemic outbreak. Due to its high transmissibility, this virus quickly spread throughout the world, causing considerable health issues. The scientific community exerted noteworthy efforts to obtain therapeutic solutions for COVID-19, and new scientific networks were constituted. No certified drugs to efficiently inhibit the virus were identified, and the development of de-novo medicines requires approximately ten years of research. Therefore, the repurposing of natural products could be an effective strategy to handle SARS-CoV-2 infection. This review aims to update on current status of the natural occurring compounds recognizing SARS-CoV-2 druggable targets. Among the clinical trials actually recruited, some natural compounds are ongoing to examine their potential role to prevent and to treat the COVID-19 infection. Many natural scaffolds, including alkaloids, terpenes, flavonoids, and benzoquinones, were investigated by in-silico, in-vitro, and in-vivo approaches. Despite the large data set obtained by a computational approach, experimental evidences in most cases are not available. To fill this gap, further efforts to validate these results are required. We believe that an accurate investigation of naturally occurring compounds may provide insights for the potential treatment of COVID-19 patients.
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Affiliation(s)
- Isabella Romeo
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
| | - Francesco Mesiti
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
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Samad MA, Saiman MZ, Abdul Majid N, Karsani SA, Yaacob JS. Berberine Inhibits Telomerase Activity and Induces Cell Cycle Arrest and Telomere Erosion in Colorectal Cancer Cell Line, HCT 116. Molecules 2021; 26:molecules26020376. [PMID: 33450878 PMCID: PMC7828342 DOI: 10.3390/molecules26020376] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the most common cancer among males and females, which is associated with the increment of telomerase level and activity. Some plant-derived compounds are telomerase inhibitors that have the potential to decrease telomerase activity and/or level in various cancer cell lines. Unfortunately, a deeper understanding of the effects of telomerase inhibitor compound(s) on CRC cells is still lacking. Therefore, in this study, the aspects of telomerase inhibitors on a CRC cell line (HCT 116) were investigated. Screening on HCT 116 at 48 h showed that berberine (10.30 ± 0.89 µg/mL) is the most effective (lowest IC50 value) telomerase inhibitor compared to boldine (37.87 ± 3.12 µg/mL) and silymarin (>200 µg/mL). Further analyses exhibited that berberine treatment caused G0/G1 phase arrest at 48 h due to high cyclin D1 (CCND1) and low cyclin-dependent kinase 4 (CDK4) protein and mRNA levels, simultaneous downregulation of human telomerase reverse transcriptase (TERT) mRNA and human telomerase RNA component (TERC) levels, as well as a decrease in the TERT protein level and telomerase activity. The effect of berberine treatment on the cell cycle was time dependent as it resulted in a delayed cell cycle and doubling time by 2.18-fold. Telomerase activity and level was significantly decreased, and telomere erosion followed suit. In summary, our findings suggested that berberine could decrease telomerase activity and level of HCT 116, which in turn inhibits the proliferative ability of the cells.
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Affiliation(s)
- Muhammad Azizan Samad
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.S.); (M.Z.S.); (S.A.K.)
| | - Mohd Zuwairi Saiman
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.S.); (M.Z.S.); (S.A.K.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Nazia Abdul Majid
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.S.); (M.Z.S.); (S.A.K.)
- Correspondence: (N.A.M.); (J.S.Y.); Tel.: +60-3-7967-5833 (N.A.M.); +60-3-7967-4090 (J.S.Y.)
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.S.); (M.Z.S.); (S.A.K.)
| | - Jamilah Syafawati Yaacob
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.S.); (M.Z.S.); (S.A.K.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (N.A.M.); (J.S.Y.); Tel.: +60-3-7967-5833 (N.A.M.); +60-3-7967-4090 (J.S.Y.)
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Nayis A, Liebl K, Frost CV, Zacharias M. Targeting Telomeres: Molecular Dynamics and Free Energy Simulation of Gold-Carbene Binding to DNA. Biophys J 2020; 120:101-108. [PMID: 33285115 DOI: 10.1016/j.bpj.2020.11.2263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 01/21/2023] Open
Abstract
DNA sequences in regulatory regions and in telomers at the ends of chromosomes frequently contain tandem repeats of guanine nucleotides that can form stacked structures stabilized by Hoogsten pairing and centrally bound monovalent cations. The replication and elongation of telomeres requires the disruption of these G-quadruplex structures. Hence, drug molecules such as gold (Au)-carbene that stabilize G-quadruplexes may also interfere with the elongation of telomeres and, in turn, could be used to control cell replication and growth. To better understand the molecular mechanism of Au-carbene binding to G-quadruplexes, we employed molecular dynamics simulations and free energy simulations. Whereas very restricted mobility of two Au-carbene ligands was found upon binding as a doublet to one side of the G-quadruplex, much larger translational and orientational mobility was observed for a single Au-carbene binding at the second G-quadruplex surface. Comparative simulations on duplex DNA in the presence of Au-carbene ligands indicates a preference for the minor groove and weaker unspecific and more salt-dependent binding than to the G-quadruplex surface. Analysis of energetic contributions reveals a dominance of nonpolar and van der Waals interactions to drive binding. The simulations can also be helpful for proposing possible modifications that could improve Au-carbene affinity and specificity for G-quadruplex binding.
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Affiliation(s)
- Asmar Nayis
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Korbinian Liebl
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Christina V Frost
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany.
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O'Hagan MP, Haldar S, Morales JC, Mulholland AJ, Galan MC. Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands. Chem Sci 2020; 12:1415-1426. [PMID: 34163904 PMCID: PMC8179204 DOI: 10.1039/d0sc05223j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.
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Affiliation(s)
- Michael P O'Hagan
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Susanta Haldar
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - Juan C Morales
- Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada Avenida del Conocimiento 17, 18016 Armilla Granada Spain
| | - Adrian J Mulholland
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - M Carmen Galan
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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Becher J, Berdnikova DV, Ihmels H, Stremmel C. Synthesis and investigation of quadruplex-DNA-binding, 9- O-substituted berberine derivatives. Beilstein J Org Chem 2020; 16:2795-2806. [PMID: 33281983 PMCID: PMC7684686 DOI: 10.3762/bjoc.16.230] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
A small series of five novel berberine derivatives was synthesized by the Cu-catalyzed click reaction of 9-propargyladenine with 9-O-(azidoalkyl)berberine derivatives. The association of the resulting berberine-adenine conjugates with representative quadruplex-forming oligonucleotides 22AG dA(G3TTA)3G3 and a2 d(ACAG4TGTG4)2 was examined with photometric and fluorimetric titrations, thermal DNA denaturation analysis, and CD spectroscopy. The results from the spectrometric titrations indicated the formation of 2:1 or 1:1 complexes (ligand:G4-DNA) with log K b values of 10-11 (2:1) and 5-6 (1:1), which are typical for berberine derivatives. Notably, a clear relationship between the binding affinity of the ligands with the length of the alkyl linker chain, n, was not observed. However, depending on the structure, the ligands exhibited different effects when bound to the G4-DNA, such as fluorescent light-up effects and formation of ICD bands, which are mostly pronounced with a linker length of n = 4 (with a2) and n = 5 (with 22AG), thus indicating that each ligand-G4-DNA complex has a specific structure with respect to relative alignment and conformational flexibility of the ligand in the binding site. It was shown exemplarily with one representative ligand from the series that such berberine-adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do not provide evidence for a significant effect of the adenine unit on the binding affinity of the ligands, for example, by additional association with the loops, presumably because the adenine residue is sterically shielded by the neighboring triazole unit.
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Affiliation(s)
- Jonas Becher
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Daria V Berdnikova
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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41
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SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations. J Comput Aided Mol Des 2020; 35:117-129. [PMID: 33037549 DOI: 10.1007/s10822-020-00351-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022]
Abstract
The prediction of host-guest binding affinities with computational modelling is still a challenging task. In the 7th statistical assessment of the modeling of proteins and ligands (SAMPL) challenge, a new host named TrimerTrip was synthesized and the thermodynamic parameters of 16 structurally diverse guests binding to the host were characterized. In the TrimerTrip-guest challenge, only structures of the host and the guests are provided, which indicates that the predictions of both the binding poses and the binding affinities are under assessment. In this work, starting from the binding poses obtained from our previous enhanced sampling simulations in the configurational space, we perform extensive alchemical and end-point free energy calculations to calculate the host-guest binding affinities retrospectively. The alchemical predictions with two widely accepted charge schemes (i.e. AM1-BCC and RESP) are in good agreement with the experimental reference, while the end-point estimates perform poorly in reproducing the experimental binding affinities. Aside from the absolute value of the binding affinity, the rank of binding free energies is also crucial in drug design. Surprisingly, the end-point MM/PBSA method seems very powerful in reproducing the experimental rank of binding affinities. Although the length of our simulations is long and the intermediate spacing is dense, the convergence behavior is not very good, which may arise from the flexibility of the host molecule. Enhanced sampling techniques in the configurational space may be required to obtain fully converged sampling. Further, as the length of sampling in alchemical free energy calculations already achieves several hundred ns, performing direct simulations of the binding/unbinding event in the physical space could be more useful and insightful. More details about the binding pathway and mechanism could be obtained in this way. The nonequilibrium method could also be a nice choice if one insists to use the alchemical method, as the intermediate sampling is avoided to some extent.
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Sullivan HJ, Chen B, Wu C. Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex. J Chem Inf Model 2020; 60:5203-5224. [PMID: 32820923 DOI: 10.1021/acs.jcim.0c00632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 K), c-KIT1 (∼27 K), and c-Myc (∼25 K). Without experimentally solved structures of these CX-5461-G4 complexes, CX-5461's interactions remain elusive. In this study, we performed a total of 73.5 μs free ligand molecular dynamics binding simulations of CX-5461 to the DNA duplex and three G4s. Three binding modes (top, bottom, and side) were identified for each system and their thermodynamic, kinetic, and structural nature were deciphered. The molecular mechanics/Poisson Boltzmann surface area binding energies of CX-5461 were calculated for the human telomeric (-28.6 kcal/mol), c-KIT1 (-23.9 kcal/mol), c-Myc (-22.0 kcal/mol) G4s, and DNA duplex (-15.0 kcal/mol) systems. These energetic differences coupled with structural differences at the 3' site explained the different melting temperatures between the G4s, while CX-5461's lack of intercalation to the duplex explained the difference between the G4s and duplex. Based on the interaction insight, CX-5461 derivatives were designed and docked, showing higher selectivity to the G4s over the duplex.
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Affiliation(s)
- Holli-Joi Sullivan
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
| | - Brian Chen
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
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Drug-like biimidazole derivatives dually target c-MYC/BCL-2 G-quadruplexes and inhibit acute myeloid leukemia. Bioorg Chem 2020; 104:104264. [PMID: 32920366 DOI: 10.1016/j.bioorg.2020.104264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 01/29/2023]
Abstract
Chemotherapy is the main approach for treating acute myeloid leukemia (AML). However, this therapy can cause severe side effects as well as drug resistance, hence calling for new therapeutic strategies. As c-MYC and BCL-2 are often overexpressed in AML, and synergism between c-MYC and BCL-2 promotes tumorigenesis, therefore, dual targeting of c-MYC/BCL-2 promoter G-quadruplexes (G4s) and then inhibiting the targeted gene expression would be a potential strategy in ALM treatment. In this work, in the search of dual ligands, we performed a screening assay with an in-house, imidazole-based compound library. Consequently, two drug-like biimidazole derivatives were identified as selective c-MYC/BCL-2 G4 binders, of which, BIM-2 was selected as the candidate for inhibiting AML cell growth. Then, BIM-2 was demonstrated to downregulate both c-MYC and BCL-2 expression, and thereby cause cell cycle arrest at G0/G1 phase and apoptosis in AML cells. Furthermore, the possible end-stacking binding modes between BIM-2 and c-MYC/BCL-2 G4s were revealed by NMR and molecular docking studies. Accordingly, this study provides a new class of drug-like dual-selective c-MYC/BCL-2 G4 ligands for the potential treatment of AML.
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Ligand binding free-energy calculations with funnel metadynamics. Nat Protoc 2020; 15:2837-2866. [PMID: 32814837 DOI: 10.1038/s41596-020-0342-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/17/2020] [Indexed: 11/09/2022]
Abstract
The accurate resolution of the binding mechanism of a ligand to its molecular target is fundamental to develop a successful drug design campaign. Free-energy calculations, which provide the energy value of the ligand-protein binding complex, are essential for resolving the binding mode of the ligand. The accuracy of free-energy calculation methods is counteracted by their poor user-friendliness, which hampers their broad application. Here we present the Funnel-Metadynamics Advanced Protocol (FMAP), which is a flexible and user-friendly graphical user interface (GUI)-based protocol to perform funnel metadynamics, a binding free-energy method that employs a funnel-shape restraint potential to reveal the ligand binding mode and accurately calculate the absolute ligand-protein binding free energy. FMAP guides the user through all phases of the free-energy calculation process, from preparation of the input files, to production simulation, to analysis of the results. FMAP delivers the ligand binding mode and the absolute protein-ligand binding free energy as outputs. Alternative binding modes and the role of waters are also elucidated, providing a detailed description of the ligand binding mechanism. The entire protocol on the paradigmatic system benzamidine-trypsin, composed of ~105 k atoms, took ~2.8 d using the Cray XC50 piz Daint cluster at the Swiss National Supercomputing Centre.
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Sun Z. SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations. J Comput Aided Mol Des 2020; 35:105-115. [PMID: 32776199 DOI: 10.1007/s10822-020-00335-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022]
Abstract
Host-guest binding remains a major challenge in modern computational modelling. The newest 7th statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and calculate the binding affinities in all three host-guest binding cases of the 6th SAMPL challenge. In this work, we report a retrospective study on the TrimerTrip host-guest systems by employing the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The calculated binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations. Note that as the work is performed after the close of the SAMPL7 challenge, we do not participate in the challenge and the results are not formally submitted to the SAMPL7 challenge.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
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Abstract
Alphaviruses are enveloped positive-sense RNA viruses that can cause serious human illnesses such as polyarthritis and encephalitis. Despite their widespread distribution and medical importance, there are no licensed vaccines or antivirals to combat alphavirus infections. Berberine chloride (BBC) is a pan-alphavirus inhibitor that was previously identified in a replicon-based small-molecule screen. This work showed that BBC inhibits alphavirus replication but also suggested that BBC might have additional effects later in the viral life cycle. Here, we show that BBC has late effects that target the virus nucleocapsid (NC) core. Infected cells treated with BBC late in infection were unable to form stable cytoplasmic NCs or assembly intermediates, as assayed by gradient sedimentation. In vitro studies with recombinant capsid protein (Cp) and purified genomic RNA (gRNA) showed that BBC perturbs core-like particle formation and potentially traps the assembly process in intermediate states. Particles produced from BBC-treated cells were less infectious, despite efficient particle production and only minor decreases in genome packaging. In addition, BBC treatment of free virus particles strongly decreased alphavirus infectivity. In contrast, the infectivity of the negative-sense RNA virus vesicular stomatitis virus was resistant to BBC treatment of infected cells or free virus. Together, our data indicate that BBC alters alphavirus Cp-gRNA interactions and oligomerization and suggest that this may cause defects in NC assembly and in disassembly during subsequent virus entry. Thus, BBC may be considered a novel alphavirus NC assembly inhibitor.IMPORTANCE The alphavirus chikungunya virus (CHIKV) is an example of an emerging human pathogen with increased and rapid global spread. Although an acute CHIKV infection is rarely fatal, many patients suffer from debilitating chronic arthralgia for years. Antivirals against chikungunya and other alphaviruses have been identified in vitro, but to date none have been shown to be efficacious and have been licensed for human use. Here, we investigated a small molecule, berberine chloride (BBC), and showed that it inhibited infectious virus production by several alphaviruses including CHIKV. BBC acted on a late step in the alphavirus exit pathway, namely the formation of the nucleocapsid containing the infectious viral RNA. Better understanding of nucleocapsid formation and its inhibition by BBC will provide important information on the mechanisms of infectious alphavirus production and may enable their future targeting in antiviral strategies.
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D’Annessa I, Di Leva FS, La Teana A, Novellino E, Limongelli V, Di Marino D. Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We? Front Mol Biosci 2020; 7:66. [PMID: 32432124 PMCID: PMC7214840 DOI: 10.3389/fmolb.2020.00066] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Peptides and peptidomimetics are strongly re-emerging as amenable candidates in the development of therapeutic strategies against a plethora of pathologies. In particular, these molecules are extremely suitable to treat diseases in which a major role is played by protein-protein interactions (PPIs). Unlike small organic compounds, peptides display both a high degree of specificity avoiding secondary off-targets effects and a relatively low degree of toxicity. Further advantages are provided by the possibility to easily conjugate peptides to functionalized nanoparticles, so improving their delivery and cellular uptake. In many cases, such molecules need to assume a specific three-dimensional conformation that resembles the bioactive one of the endogenous ligand. To this end, chemical modifications are introduced in the polypeptide chain to constrain it in a well-defined conformation, and to improve the drug-like properties. In this context, a successful strategy for peptide/peptidomimetics design and optimization is to combine different computational approaches ranging from structural bioinformatics to atomistic simulations. Here, we review the computational tools for peptide design, highlighting their main features and differences, and discuss selected protocols, among the large number of methods available, used to assess and improve the stability of the functional folding of the peptides. Finally, we introduce the simulation techniques employed to predict the binding affinity of the designed peptides for their targets.
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Affiliation(s)
- Ilda D’Annessa
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | | | - Anna La Teana
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
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48
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Song D, Hao J, Fan D. Biological properties and clinical applications of berberine. Front Med 2020; 14:564-582. [DOI: 10.1007/s11684-019-0724-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023]
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49
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Khanna L, Singhal S, Jain SC, Khanna P. Spiro-Indole-Coumarin Hybrids: Synthesis, ADME, DFT, NBO Studies and In Silico Screening through Molecular Docking on DNA G-Quadruplex. ChemistrySelect 2020; 5:3420-3433. [PMID: 32328514 PMCID: PMC7169502 DOI: 10.1002/slct.201904783] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/09/2020] [Indexed: 01/11/2023]
Abstract
New series of hybrids were synthesized by combination of 4-hydroxycoumarin with spiro[indol-indazole-thiazolidine]-diones and spiro[indol-pyrazole-thiazolidine]-diones, via hitherto unknown Schiff bases. The effects of substituents, such as -F, -Br and -CH3, on the crucial characteristics pertaining to the hybrids were investigated through computational studies. In silico or virtual screening through molecular docking studies on the library of 22 compounds, including reference compounds, precursors, non-hybrid and hybrid derivatives, was performed on DNA G-quadruplex of the human genome. All six freshly synthesized hybrids showed high binding energy as compared to non-hybrids as well as reference compounds. The presence of substituents at 5-position of indole enhanced the binding tendency of the ligand. ADME studies indicated good oral bioavailability and absorption of these compounds. Density Functional Theory (DFT) calculations of hybrids were done at B3LYP/6-311G++(d,p) level of computation. Their HOMO and LUMO energy plots reflected the presence of high charge transfer and chemical potential. Natural bond order (NBO) calculations predicted hyperconjugative interactions. The Molecular Electrostatic Potential (MEP) surface plots showed possible electrophilic and nucleophilic attacking sites of the hybrids. Compound 10 a (5-fluoro-spiro[indol-indazole-thiazolidine]-dione-coumarin hybrid), on the basis of global reactivity descriptors, was filtered to be chemically most reactive with the highest binding energy of -8.23 kcal/mol with DNA G-quadruplex. The synthesized hybrid coumarin derivatives in correlation with theoretical docking studies validate that hybrid derivatives are more reactive compared to their non-hybrid counterparts.
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Affiliation(s)
- Leena Khanna
- Department of ChemistryUniversity of DelhiDelhi110007India
- University School of Basic and Applied SciencesGuru Gobind Singh Indraprastha University, Sector 16-C, DwarkaNew Delhi110078India
| | - Sugandha Singhal
- University School of Basic and Applied SciencesGuru Gobind Singh Indraprastha University, Sector 16-C, DwarkaNew Delhi110078India
| | | | - Pankaj Khanna
- Department of ChemistryUniversity of DelhiDelhi110007India
- Department of ChemistryAcharya Narendra Dev CollegeUniversity of Delhi, KalkajiNew Delhi110019India
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Cruz J, Wickstrom L, Yang D, Gallicchio E, Deng N. Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites. J Chem Theory Comput 2020; 16:2803-2813. [PMID: 32101691 DOI: 10.1021/acs.jctc.9b01119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a new approach to more accurately and efficiently compute the absolute binding free energy for receptor-ligand complexes. Currently, the double decoupling method (DDM) and the potential of mean force method (PMF) are widely used to compute the absolute binding free energy of biomolecular complexes. DDM relies on alchemically decoupling the ligand from its environments, which can be computationally challenging for large ligands and charged ligands because of the large magnitude of the decoupling free energies involved. In contrast, the PMF method uses a physical pathway to directly transfer the ligand from solution to the receptor binding pocket and thus avoids some of the aforementioned problems in DDM. However, the PMF method has its own drawbacks: because of its reliance on a ligand binding/unbinding pathway that is free of steric obstructions from the receptor atoms, the method has difficulty treating ligands with buried atoms. To overcome the limitation in the standard PMF approach and enable buried ligands to be treated, here we develop a new method called AlchemPMF in which steric obstructions along the physical pathway for binding are alchemically removed. We have tested the new approach on two important drug targets involving charged ligands. One is HIV-1 integrase bound to an allosteric inhibitor; the other is the human telomeric DNA G-quadruplex in complex with a natural product protoberberine buried in the binding pocket. For both systems, the new approach leads to more reliable estimates of absolute binding free energies with smaller error bars and closer agreements with experiments compared with those obtained from the existing methods, demonstrating the effectiveness of the new method in overcoming the hysteresis often encountered in PMF binding free energy calculations of such systems. The new approach could also be used to improve the sampling of water equilibration and resolvation of the binding pocket as the ligand is extracted.
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Affiliation(s)
- Jeffrey Cruz
- Department of Chemistry and Physical Sciences, Pace University, New York, New York 10038, United States
| | - Lauren Wickstrom
- Department of Science, Borough of Manhattan Community College, The City University of New York, New York, New York 10007, United States
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, New York 11210, United States.,Ph.D. Program in Biochemistry, Graduate Center, City University of New York, New York, New York 10016, United States.,Ph.D. Program in Chemistry, Graduate Center, City University of New York, New York, New York 10016, United States
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, New York 10038, United States
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