Category: Publications

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The Biofilms Structural Database

Check our recent publication about “The Biofilms Structural Database”, a database devoted to the proteins involved in the biofilms’ formation.

Abstract

The Biofilms Structural Database (BSD) is a collection of structural, mutagenesis, kinetics, and inhibition data to understand the processes involved in biofilm formation. Presently, it includes curated information on 425 structures of proteins and enzymes involved in biofilm formation and development for 42 different bacteria. It is available at www.biofilms.biosim.pt.

Authors: Magalhães RP, Vieira TF, Fernandes HS, Melo A, Simões M, and Sousa SF

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Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges

Our recent review about studying enzymatic mechanisms using QM/MM mythologies has just been accepted on Israel Journal of Chemistry.

Abstract

Quantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐established alternative for the study of enzymatic reaction mechanisms. They enable the description of a small part of the enzyme, where reactions take place through QM, while the majority of the thousands of atoms that comprise these biomolecules are handled through MM. While different “flavors” and variations in the QM/MM field exist, this review will focus more on the application of the ONIOM methodology, presenting a fresh perspective on the application of this popular method in light of the growth in computational power and level of sophistication of the different methodologies that it can combine. In addition to a brief presentation of the basic principles behind these methods, this review will discuss different examples of applicability, common choices, practical considerations, and main problems involved, stemming from our experience in this field. Finally, a reflection on the future challenges for the next decade in the QM/MM modeling of enzymatic mechanisms is presented.

Authors: Magalhães RP, Fernandes HS, and Sousa SF

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VMD Store – a VMD Plugin to Browse, Discover, and Install VMD Extensions

Henrique Silva Fernandes, Sérgio F. Sousa, and Nuno M.F.S.A. Cerqueira

Published on 21st October 2019
Journal: Journal of Chemical Information and Modeling

https://doi.org/10.1021/acs.jcim.9b00739 | Download citation

Abstract

Herein we present the VMD Store, an open-source VMD plugin that simplifies the way how users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism to install and configure VMD extensions. This plugin arises in an attempt to aggregate all VMD extensions in a single platform. The VMD Store is available, free of charge, for Windows, macOS, and Linux at https://biosim.pt/software/, and requires VMD 1.9.3 (or later).

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Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

Henrique S. Fernandes, Sérgio F. Sousa, and Nuno M.F.S.A. Cerqueira

Journal: Molecules

https://doi.org/10.3390/molecules24132462

Abstract

Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.

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The catalytic mechanism of the Serine Hydroxymethyltransferase – a computational ONIOM QM/MM study

Henrique Silva Fernandes, Maria João Ramos, and Nuno M.F.S.A. Cerqueira

Published on 18th September 2018
Journal: ACS Catalysis

http://dx.doi.org/10.1021/acscatal.8b02321 | Download citation

Abstract

Serine Hydroxymethyltransferase (SHMT) is an important drug target to fight malaria – one of the most devastating infectious diseases that accounted in 2016 with 216 million new cases and almost 450 thousand deaths. In this paper, computational studies were carried out to unveil the catalytic mechanism of SHMT using QM/MM methodologies. This enzyme is responsible for the extraordinary cyclisation of a tetrahydrofolate (THF) into 5,10-methylene-THF. This process is catalyzed by a pyridoxal-5’-phosphate (PLP) cofactor that binds L-serine and from which one molecule of L-glycine is produced. The results show that the catalytic process takes place in eight sequential steps that involve an α-elimination, the cyclization of the 5-hydroxymethyl-THF intermediate into 5,10-methylene-THF and the protonation of the quinonoid intermediate. According to the calculated energetic profile, the rate-limiting step of the full mechanism is the elimination of the hydroxymethyl group, from which results a formaldehyde intermediate that then becomes covalently bonded to the THF cofactor. The calculated barrier (DLPNO-CCSD(T)/CBS:ff99SB) for the rate-limiting step (18.0 kcal/mol) agrees very well with the experimental kinetic results (15.7-16.2 kcal/mol). The results also highlight the key role played by Glu57 during the full catalytic process and particularly in the first step of the mechanism that requires an anionic Glu57, contrasting with some proposals available in the literature for this step. It was also concluded that the cyclisation of THF must take place in the enzyme, rather than in solution as it has been proposed also in the past. All of these results together provide new knowledge and insight on the catalytic mechanism of SHMT that now can be used to develop new inhibitors targeting SHMT and therefore new anti-malaria drugs.

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molUP is cover of the Journal of Computational Chemistry 39(19)

Cover

First published: 10 June 2018 | https://doi.org/10.1002/jcc.25372

Abstract

The molUP plugin, developed by Nuno Sousa Cerqueira and colleagues and described on page 1344, overcomes some of the most common problems in computational chemistry concerning the analysis of big data. MolUP was developed for use in the analysis of quantum chemistry (QM), QM/MM (molecular mechanics), and QM/QM calculations, molecular dynamics (MD) simulations, as well as the preparation of input files. MolUP also provides new tools to analyze and visualize existing computational chemistry information in a more userfriendly way that simplifies the current complex and time‐demanding practices used in the field. (DOI: 10.1002/jcc.25189)

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molUP: a VMD plugin to handle QM and ONIOM calculations using the Gaussian software

Henrique Silva Fernandes, Maria João Ramos, and Nuno M.F.S.A. Cerqueira

Published on 21st February 2018
DOI: http://dx.doi.org/10.1002/jcc.25189 | Download citation

Abstract

The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations. The starting structures for these calculations can be imported from different chemical formats. A set of tools is available to help the user to examine or modify any geometry parameter. This includes the definition of layers in ONIOM calculations, choosing fixed atoms during geometry optimizations, the recalculation or adjustment of the atomic charges, performing SCANs or IRC calculations, etc. molUP also extracts the geometries from the output files as well as the energies of each of them. All of these tasks are performed in an interactive GUI that is extremely helpful for the user. MolUP was developed to be easy to handle by inexperienced users, but simultaneously to be a fast and flexible graphical interface to allow the advanced users to take full advantage of this plugin. The program is available, free of charges, for macOS, Linux, and Windows at the PortoBioComp page https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup.

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The Catalytic Mechanism of the Pyridoxal-5′-phosphate-Dependent Enzyme, Histidine Decarboxylase: A Computational Study

Henrique Silva Fernandes, Maria João Ramos, and Nuno M.F.S.A. Cerqueira

Published on June 14th 2017
DOI: http://dx.doi.org/10.1002/chem.201701375 | Download citation

Abstract

The catalytic mechanism of histidine decarboxylase (HDC), a pyridoxal-5′-phosphate (PLP)-dependent enzyme, was studied by using a computational QM/MM approach following the scheme M06-2X/6–311++G(3df,2pd):Amber. The reaction involves two sequential steps: the decarboxylation of l-histidine and the protonation of the generated intermediate from which results histamine. The rate-limiting step is the first one (ΔG≠=17.6 kcal mol−1; ΔGr=13.7 kcal mol−1) and agrees closely with the available experimental kcat (1.73 s−1), which corresponds to an activation barrier of 17.9 kcal mol−1. In contrast, the second step is very fast (ΔG≠=1.9 kcal mol−1) and exergonic (ΔGr=−33.2 kcal mol−1). Our results agree with the available experimental data and allow us to explain the role played by several active site residues that are considered relevant according to site-directed mutagenesis studies, namely Tyr334B, Asp273A, Lys305A, and Ser354B. These results can provide insights regarding the catalytic mechanism of other enzymes belonging to family II of PLP-dependent decarboxylases.

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Nanostructures for Cancer Therapy – Elsevier

Editors: Alexandru Grumezescu Anton Ficai
eBook ISBN: 9780323461504
Hardcover ISBN: 9780323461443
Imprint: Elsevier
Published Date: 14th April 2017
Page Count: 920
DOI: 10.1016/B978-0-323-46144-3.00024-6

Nanostructures for Cancer Therapy discusses the available preclinical and clinical nanoparticle technology platforms and their impact on cancer therapy, including current trends and developments in the use of nanostructured materials in chemotherapy and chemotherapeutics.

In particular, coverage is given to the applications of gold nanoparticles and quantum dots in cancer therapies. In addition to the multifunctional nanomaterials involved in the treatment of cancer, other topics covered include nanocomposites that can target tumoral cells and the release of antitumoral therapeutic agents.

The book is an up-to-date overview that covers the inorganic and organic nanostructures involved in the diagnostics and treatment of cancer.

Chapter 24 – Cancer Therapies Based on Enzymatic Amino Acid Depletion

Carla Teixeira*, Henrique Fernandes*, P. A. Fernandes, M. J. Ramos and Nuno M. F. S. A. Cerqueira (* contributed equally to this work)

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Abstract

A growing understanding of tumor biology has allowed the identification of various cellular characteristics that are more frequently associated with cancer cells than with normal cells. These findings have prompted the development of new therapeutics specifically designed to exploit these differences. In this context, the amino acid depriving enzymes have shown very promising results and proven to be active and very specific against various types of cancers. These therapies involve the depletion of specific amino acids in the bloodstream that cannot be synthesized by tumor cells. This happens because these cells often have a defecting enzymatic armamentarium and therefore rely on external supply for those amino acids. Decreasing the concentration of certain amino acids in blood has thus been shown to impair the development or even destroy tumor cells. Normal cells remain unaltered since they are less demanding and/or can synthesize these compounds in sufficient amounts by other mechanisms.

In this chapter, the structure, function, catalytic mechanism and therapeutic application of some amino acid depriving enzymes will be reviewed. Particular attention will be given to enzymes that have potential or are currently used in the treatment of several types of cancer, namely: (1) l-asparaginase used for the treatment of acute lymphoblastic leukemia; (2) l-arginase and l-arginine deiminase that are used in the therapy of hepatocellular carcinomas and melanomas, two diseases that account annually with approximately 1 million of new cases and for which there is currently no efficacious treatment; and (3) l-Methioninase with potential to be used in the treatment of breast, colon, lung, and renal cancers.

Keywords

  • amino acid deprivation;
  • heterologous enzymes;
  • tumor;
  • cancer;
  • catalytic mechanism;
  • asparaginase;
  • methioninase;
  • arginase;
  • arginine deaminase
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Amino Acid Deprivation Using Enzymes as a Targeted Therapy for Cancer and Viral Infections

Pages 283-297 | Received 29 Jul 2016, Accepted 25 Oct 2016, Accepted author version posted online: 04 Nov 2016, Published online: 15 Nov 2016

ABSTRACT

Introduction: Amino acid depletion in the blood serum is currently being exploited and explored for therapies in tumors or viral infections that are auxotrophic for a certain amino acid or have a metabolic defect and cannot produce it. The success of these treatments is because normal cells remain unaltered since they are less demanding and/or can synthesize these compounds in sufficient amounts for their needs by other mechanisms.

Areas covered: This review is focused on amino acid depriving enzymes and their formulations that have been successfully used in the treatment of several types of cancer and viral infections. Particular attention will be given to the enzymes L-asparaginase, L-arginase, L-arginine deiminase, and L-methionine-γ-lyase.

Expert opinion: The immunogenicity and other toxic effects are perhaps the major limitations of these therapies, but they have been successfully decreased either through the expression of these enzymes from other organisms, recombination processes, pegylation of the selected enzymes or by specific mutations in the proteins. In 2006, FDA has already approved the use of L-asparaginase in the treatment of acute lymphoblastic leukemia. Other enzymes and in particular L-arginase, L-arginine deiminase, and L-methioninase have been showing promising results in vitro and in vivo studies.

KEYWORDS: Amino acid deprivation, L-asparaginase, L-methioninase, L-arginase, L-arginine deiminase, cancer, viral infections