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Biomolecules
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Biomolecular Structure and Drug Design. Advances in Therapy against Neglected...
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Biomolecular Structure and Drug Design. Advances in Therapy against Neglected Infectious Diseases

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Structure and Dynamics".

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 12936

Special Issue Editors

Dr. Alfonso T. Garcia-Sosa

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Guest Editor
Senior Research Fellow, Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
Special Issues, Collections and Topics in MDPI journals
Dr. Paul Nguewa

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Guest Editor
ISTUN Instituto de Salud Tropical and Department of Microbiology and Parasitology, Universidad de Navarra Edif. Ciencias, C/ Irunlarrea, 1, E-31008 Pamplona (Navarra), Spain

Special Issue Information

Dear Colleagues,

Neglected infectious diseases (NIDs) exhibit chronic, disfiguring, and stigmatizing impacts. Such effects also threaten the achievement of the Millennium Development Goals (MDGs) and Sustainable Development Goals (SDGs). Individuals are often infected with multiple NIDs simultaneously. They represent one-sixth of the world’s population. In fact, more than a billion people are infected with one or more NIDs, causing 180,000 deaths each year, and an additional two billion are at risk. Several innovative approaches may allow for the future availability of safe and effective treatments for the most prevalent NIDs.

At the same time, recent advances in drug design are making the prediction and elucidation of biomolecular targets possible, as well as their interactions with other molecules and their mechanisms of action. Topics including bio- and chemo-informatics, small-molecule and peptide drugs and modulators, machine-learning, and peptidomimetic compounds applied to drug discovery and chemical biology are forthcoming, and may help improve on the knowledge and development of new treatments.

This Special Issue will cover the current advances in small-molecule and biologic therapy against NIDs, biomolecular structure and drug design, and all of the relevant aspects for the development and expansion of novel chemical and biomolecular NID treatments. This Special Issue will include review articles and original research articles in this field.

Dr. Alfonso T. Garcia-Sosa
Dr. Paul Nguewa
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biomolecular structure and drug design
  • Chemo-informatics
  • Machine-learning
  • Drug discovery
  • Neglected diseases
  • Structure prediction
  • Small-molecule and peptide drugs
  • Peptidomimetic drugs
  • Therapeutic targets

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Published Papers (3 papers)

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Research

21 pages, 1616 KiB  
Article
Comparative Characterization of Plasmodium falciparum Hsp70-1 Relative to E. coli DnaK Reveals the Functional Specificity of the Parasite Chaperone
by Charity Mekgwa Lebepe, Pearl Rutendo Matambanadzo, Xolani Henry Makhoba, Ikechukwu Achilonu, Tawanda Zininga and Addmore Shonhai
Biomolecules 2020, 10(6), 856; https://doi.org/10.3390/biom10060856 - 4 Jun 2020
Cited by 20 | Viewed by 3189
Abstract
Hsp70 is a conserved molecular chaperone. How Hsp70 exhibits specialized functions across species remains to be understood. Plasmodium falciparum Hsp70-1 (PfHsp70-1) and Escherichia coli DnaK are cytosol localized molecular chaperones that are important for the survival of these two organisms. In the current [...] Read more.
Hsp70 is a conserved molecular chaperone. How Hsp70 exhibits specialized functions across species remains to be understood. Plasmodium falciparum Hsp70-1 (PfHsp70-1) and Escherichia coli DnaK are cytosol localized molecular chaperones that are important for the survival of these two organisms. In the current study, we investigated comparative structure-function features of PfHsp70-1 relative to DnaK and a chimeric protein, KPf, constituted by the ATPase domain of DnaK and the substrate binding domain (SBD) of PfHsp70-1. Recombinant forms of the three Hsp70s exhibited similar secondary and tertiary structural folds. However, compared to DnaK, both KPf and PfHsp70-1 were more stable to heat stress and exhibited higher basal ATPase activity. In addition, PfHsp70-1 preferentially bound to asparagine rich peptide substrates, as opposed to DnaK. Recombinant P. falciparum adenosylmethionine decarboxylase (PfAdoMetDC) co-expressed in E. coli with either KPf or PfHsp70-1 was produced as a fully folded product. Co-expression of PfAdoMetDC with heterologous DnaK in E. coli did not promote folding of the former. However, a combination of supplementary GroEL plus DnaK improved folding of PfAdoMetDC. These findings demonstrated that the SBD of PfHsp70-1 regulates several functional features of the protein and that this molecular chaperone is tailored to facilitate folding of plasmodial proteins. Full article
(This article belongs to the Special Issue Biomolecular Structure and Drug Design. Advances in Therapy against Neglected Infectious Diseases)
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28 pages, 9993 KiB  
Article
The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major May Be Involved in the Resistance to Drugs such as Paromomycin
by Andrés Vacas, Celia Fernández-Rubio, Miriam Algarabel, José Peña-Guerrero, Esther Larrea, Fabio Rocha Formiga, Alfonso T. García-Sosa and Paul A. Nguewa
Biomolecules 2019, 9(11), 723; https://doi.org/10.3390/biom9110723 - 11 Nov 2019
Cited by 8 | Viewed by 4174
Abstract
The identification and clarification of the mechanisms of action of drugs used against leishmaniasis may improve their administration regimens and prevent the development of resistant strains. Herein, for the first time, we describe the structure of the putatively essential Ser/Thr kinase LmjF.22.0810 from [...] Read more.
The identification and clarification of the mechanisms of action of drugs used against leishmaniasis may improve their administration regimens and prevent the development of resistant strains. Herein, for the first time, we describe the structure of the putatively essential Ser/Thr kinase LmjF.22.0810 from Leishmania major. Molecular dynamics simulations were performed to assess the stability of the kinase model. The analysis of its sequence and structure revealed two druggable sites on the protein. Furthermore, in silico docking of small molecules showed that aminoglycosides preferentially bind to the phosphorylation site of the protein. Given that transgenic LmjF.22.0810-overexpressing parasites displayed less sensitivity to aminoglycosides such as paromomycin, our predicted models support the idea that the mechanism of drug resistance observed in those transgenic parasites is the tight binding of such compounds to LmjF.22.0810 associated with its overexpression. These results may be helpful to understand the complex machinery of drug response in Leishmania. Full article
(This article belongs to the Special Issue Biomolecular Structure and Drug Design. Advances in Therapy against Neglected Infectious Diseases)
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18 pages, 3250 KiB  
Article
Zika and Flavivirus Shell Disorder: Virulence and Fetal Morbidity
by Gerard Kian-Meng Goh, A. Keith Dunker, James A. Foster and Vladimir N. Uversky
Biomolecules 2019, 9(11), 710; https://doi.org/10.3390/biom9110710 - 6 Nov 2019
Cited by 23 | Viewed by 4385
Abstract
Zika virus (ZIKV) was first discovered in 1947 in Africa. Since then, sporadic ZIKV infections of humans have been reported in Africa and Asia. For a long time, this virus was mostly unnoticed due to its mild symptoms and low fatality rates. However, [...] Read more.
Zika virus (ZIKV) was first discovered in 1947 in Africa. Since then, sporadic ZIKV infections of humans have been reported in Africa and Asia. For a long time, this virus was mostly unnoticed due to its mild symptoms and low fatality rates. However, during the 2015–2016 epidemic in Central and South America, when millions of people were infected, it was discovered that ZIKV causes microcephaly in the babies of mothers infected during pregnancy. An examination of the M and C proteins of the ZIKV shell using the disorder predictor PONDR VLXT revealed that the M protein contains relatively high disorder levels comparable only to those of the yellow fever virus (YFV). On the other hand, the disorder levels in the C protein are relatively low, which can account for the low case fatality rate (CFR) of this virus in contrast to the more virulent YFV, which is characterized by high disorder in its C protein. A larger variation was found in the percentage of intrinsic disorder (PID) in the C protein of various ZIKV strains. Strains of African lineage are characterized by higher PIDs. Using both in vivo and in vitro experiments, laboratories have also previously shown that strains of African origin have a greater potential to inflict higher fetal morbidity than do strains of Asian lineage, with dengue-2 virus (DENV-2) having the least potential. Strong correlations were found between the potential to inflict fetal morbidity and shell disorder in ZIKV (r2 = 0.9) and DENV-2 (DENV-2 + ZIKV, r2 = 0.8). A strong correlation between CFR and PID was also observed when ZIKV was included in an analysis of sets of shell proteins from a variety of flaviviruses (r2 = 0.8). These observations have potential implications for antiviral vaccine development and for the design of cancer therapeutics in terms of developing therapeutic viruses that penetrate hard-to-reach organs. Full article
(This article belongs to the Special Issue Biomolecular Structure and Drug Design. Advances in Therapy against Neglected Infectious Diseases)
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