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Article ; Online: In silico

Atanda, Halimat / Balogun, Toheeb Adewale / Alshehri, Mohammed M / Olivos-Ramirez, Gustavo / Vilca-Quispe, Julissa / Chenet-Zuta, Manuel / Cárdenas-Cárdenas, Reyna / Delgado Wong, Henry / Ropón-Palacios, Georcki / Umar, Haruna Isiyaku

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 20, Page(s) 10713–10724

Abstract: Gastric ulcer is associated with weakening of the mucous coating of the stomach and damages to the intestinal lining. It is caused ... ...

Abstract	Gastric ulcer is associated with weakening of the mucous coating of the stomach and damages to the intestinal lining. It is caused by
MeSH term(s)	Humans ; Stomach Ulcer/chemically induced ; Stomach Ulcer/drug therapy ; Helicobacter Infections/drug therapy ; Omeprazole/pharmacology ; Omeprazole/therapeutic use ; Molecular Dynamics Simulation ; Molecular Docking Simulation
Chemical Substances	Omeprazole (KG60484QX9)
Language	English
Publishing date	2022-12-26
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2160814
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Article ; Online: Novel multi-epitope protein containing conserved epitopes from different Leishmania species as potential vaccine candidate: Integrated immunoinformatics and molecular dynamics approach.

Ropón-Palacios, Georcki / Chenet-Zuta, Manuel E / Otazu, Kewin / Olivos-Ramirez, Gustavo E / Camps, Ihosvany

Computational biology and chemistry

2019 Volume 83, Page(s) 107157

Abstract: Leishmaniosis, caused by intracellular parasites of the genus Leishmania, has become a serious public health problem around the world, and for which there are currently extensive limitations. In this work, a theoretical model was proposed for the ... ...

Abstract	Leishmaniosis, caused by intracellular parasites of the genus Leishmania, has become a serious public health problem around the world, and for which there are currently extensive limitations. In this work, a theoretical model was proposed for the development of a multi-epitope vaccine. The protein GP63 of the parasite was selected for epitopes prediction, due to its important biological role for the infection process and abundance. IEDB tools were used to determine epitopes B and T in Leishmania braziliensis; besides, other conserved epitopes in three species were selected. To improve immunogenicity, 50S ribosomal protein L7 / L12 (ID: P9WHE3) was used as a domain of adjuvant in the assembly process. The folding arrangement of the vaccine was obtained through homologous modeling multi-template with MODELLER v9.21, and a Ramachandran plot analysis was done. Furthermore, physicochemical properties were described with the ProtParam tool and secondary structure prediction combining GOR-IV and SOPMA tools. Finally, a molecular dynamics simulation (50 ns) was performed to establish flexibility and conformational changes. The analysis of the results indicates high conservancy in the epitopes predicted among the four species. Moreover, Ramachandran plot, physicochemical parameters, and secondary structure prediction suggest a stable conformation of the vaccine, after a minimum conformational change that was evaluated with the free energy landscape. The conformational change does not drive any substantial change for epitope exposition on the surface. The vaccine proposed could be tested experimentally to guide new approaches in the development of pan-vaccines; vaccines with regions conserved in multiple species.
MeSH term(s)	Epitopes/chemistry ; Epitopes/immunology ; Leishmania/immunology ; Metalloendopeptidases/chemistry ; Metalloendopeptidases/immunology ; Molecular Dynamics Simulation ; Protein Conformation ; Species Specificity ; Vaccines/immunology
Chemical Substances	Epitopes ; Vaccines ; Metalloendopeptidases (EC 3.4.24.-) ; glycoprotein gp63, Leishmania (EC 3.4.24.-)
Language	English
Publishing date	2019-11-02
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2019.107157
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2.

Ropón-Palacios, Georcki / Pérez-Silva, Jhon / Rojas-Humpire, Ricardo / Olivos-Ramírez, Gustavo E / Chenet-Zuta, Manuel / Cornejo-Villanueva, Victor / Carmen-Sifuentes, Sheyla / Otazu, Kewin / Ramirez-Díaz, Yaritza L / Chozo, Karolyn Vega / Camps, Ihosvany

Computational biology and chemistry

2022 Volume 98, Page(s) 107668

Abstract: The emergence of COVID-19 caused by SARS-CoV-2 and its spread since 2019 represents the major public health problem worldwide nowadays, which has generated a high number of infections and deaths. The spike protein (S protein) is the most studied protein ... ...

Abstract	The emergence of COVID-19 caused by SARS-CoV-2 and its spread since 2019 represents the major public health problem worldwide nowadays, which has generated a high number of infections and deaths. The spike protein (S protein) is the most studied protein of SARS-CoV-2, and key to host-cell entry through ACE2 receptor. This protein presents a large pattern of glycosylations with important roles in immunity and infection mechanisms. Therefore, understanding key aspects of the molecular mechanisms of these structures, during drug recognition in SARS-CoV-2, may contribute to therapeutic alternatives. In this work, we explored the impact of glycosylations on the drug recognition on two domains of the S protein, the receptor-binding domain (RBD) and the N-terminal domain (NTD) through molecular dynamics simulations and computational biophysics analysis. Our results show that glycosylations in the S protein induce structural stability and changes in rigidity/flexibility related to the number of glycosylations in the structure. These structural changes are important for its biological activity as well as the correct interaction of ligands in the RBD and NTD regions. Additionally, we evidenced a roto-translation phenomenon in the interaction of the ligand with RBD in the absence of glycosylation, which disappears due to the influence of glycosylation and the convergence of metastable states in RBM. Similarly, glycosylations in NTD promote an induced fit phenomenon, which is not observed in the absence of glycosylations; this process is decisive for the activity of the ligand at the cryptic site. Altogether, these results provide an explanation of glycosylation relevance in biophysical properties and drug recognition to S protein of SARS-CoV-2, which must be considered in the rational drug development and virtual screening targeting S protein.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19 ; Glycoproteins ; Glycosylation ; Humans ; Ligands ; Molecular Dynamics Simulation ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Glycoproteins ; Ligands ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-03-23
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2022.107668
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Article ; Online: Potential novel inhibitors against emerging zoonotic pathogen

Ropón-Palacios, Georcki / Chenet-Zuta, Manuel E / Olivos-Ramirez, Gustavo E / Otazu, Kewin / Acurio-Saavedra, Jorge / Camps, Ihosvany

Journal of biomolecular structure & dynamics

2019 Volume 38, Issue 11, Page(s) 3225–3234

Abstract: Nipah virus is a pathogen considered highly infectious, and its lethality can cause between 40% and 70% of deaths in those infected. At present, no effective treatment is available which results in an imperative need to explore new approaches to the ... ...

Abstract	Nipah virus is a pathogen considered highly infectious, and its lethality can cause between 40% and 70% of deaths in those infected. At present, no effective treatment is available which results in an imperative need to explore new approaches to the search for drugs. Through virtual screening techniques, docking and molecular dynamics, 183 ligands were evaluated against the Nipah virus glycoprotein (NiV-G), involved throughout the process of virus entry to the host cell, resulting in a good target for blocking the infection. Of the 183 drugs computationally screened, three of them (MMV020537, MMV688888 and MMV019838) were found to be potential inhibitors of NiV-G. Their calculated dissociation constants were 0.03 nM, 2.18 nM and 31.61 nM, respectively. Molecular dynamics studies confirm their stability binding modes in the active site of the protein. These potential inhibitors can be used later as leads for the development of new drugs that allow effective treatment of the disease.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Ligands ; Molecular Dynamics Simulation ; Nipah Virus ; Virus Internalization
Chemical Substances	Ligands
Language	English
Publishing date	2019-08-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2019.1655480
Database	MEDical Literature Analysis and Retrieval System OnLINE

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ab Jg. 2022: Lesesaal (EG)

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Article: Targeting Receptor Binding Domain and Cryptic Pocket of Spike glycoprotein from SARS-CoV-2 by biomolecular modeling

Otazu, Kewin / Chenet-Zuta, Manuel E. / Ropon-Palacios, Georcki / Olivos-Ramirez, Gustavo E. / Jimenez-Avalos, Gabriel M. / Osorio-Mogollon, Cleidy / Sosa-Amay, Frida / Vargas-Rodriguez, Rosa / Nina-Larico, Tania P. / Concu, Riccardo / Camps, Ihosvany

Abstract: SARS-CoV-2, the causative agent of the disease known as Covid-19, has so far reported around 3,435,000 cases of human infections, including more than 239,000 deaths in 187 countries, with no effective treatment currently available. For this reason, it is ...

Abstract	SARS-CoV-2, the causative agent of the disease known as Covid-19, has so far reported around 3,435,000 cases of human infections, including more than 239,000 deaths in 187 countries, with no effective treatment currently available. For this reason, it is necessary to explore new approaches for the development of a drug capable of inhibiting the entry of the virus into the host cell. Therefore, this work includes the exploration of potential inhibitory compounds for the Spike protein of SARS-CoV-2 (PDB ID: 6VSB), which were obtained from The Patogen Box. Later, they were filtered through virtual screening and molecular docking techniques, thus obtaining a top of 1000 compounds, which were used against a binding site located in the Receptor Binding Domain (RBD) and a cryptic site located in the N-Terminal Domain (NTD), resulting in good pharmaceutical targets for the blocking the infection. From the top 1000, the best compound (TCMDC-124223) was selected for the binding site. It interacts with specific residues that intervene in the recognition and subsequent entry into the host cell, resulting in a more favorable binding free energy in comparison to the control compounds (Hesperidine and Emodine). In the same way, the compound TCMDC-133766 was selected for the cryptic site. These identified compounds are potential inhibitors that can be used for the development of new drugs that allow effective treatment for the disease.
Keywords	covid19
Publisher	ArXiv
Document type	Article
Database	COVID19

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Book ; Online: Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

Osorio-Mogollon, Cleidy / Olivos-Ramirez, Gustavo E. / Otazu, Kewin / Chenet-Zuta, Manuel E. / Ropon-Palacios, Georcki / Camps, Ihosvany / Jimenez-Avalo, Gabriel M. / Apari-Cossio, Eduardo / Torres-Moreira, Natalia E. / Cardenas-Cardenas, Reyna G.

2020

Abstract: The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesis ... of genetic material ... ...

Abstract	The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesis of genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNA polymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drug search, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning is considered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria, which were filtered under the criteria of selecting those that do not present any violation of Lipinski's Rule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in in silico and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can be considered as drugs for the development of effective treatments against this new pandemic.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12501791.v1
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

2020

Abstract	The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesis of genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNA polymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drug search, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning is considered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria, which were filtered under the criteria of selecting those that do not present any violation of Lipinski's Rule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in in silico and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can be considered as drugs for the development of effective treatments against this new pandemic.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12501791
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: Targeting Receptor Binding Domain and Cryptic Pocket of Spike glycoprotein from SARS-CoV-2 by biomolecular modeling

2020

Abstract	SARS-CoV-2, the causative agent of the disease known as Covid-19, has so far reported around 3,435,000 cases of human infections, including more than 239,000 deaths in 187 countries, with no effective treatment currently available. For this reason, it is necessary to explore new approaches for the development of a drug capable of inhibiting the entry of the virus into the host cell. Therefore, this work includes the exploration of potential inhibitory compounds for the Spike protein of SARS-CoV-2 (PDB ID: 6VSB), which were obtained from The Patogen Box. Later, they were filtered through virtual screening and molecular docking techniques, thus obtaining a top of 1000 compounds, which were used against a binding site located in the Receptor Binding Domain (RBD) and a cryptic site located in the N-Terminal Domain (NTD), resulting in good pharmaceutical targets for the blocking the infection. From the top 1000, the best compound (TCMDC-124223) was selected for the binding site. It interacts with specific residues that intervene in the recognition and subsequent entry into the host cell, resulting in a more favorable binding free energy in comparison to the control compounds (Hesperidine and Emodine). In the same way, the compound TCMDC-133766 was selected for the cryptic site. These identified compounds are potential inhibitors that can be used for the development of new drugs that allow effective treatment for the disease.
Keywords	Quantitative Biology - Biomolecules ; covid19
Subject code	540
Publishing date	2020-06-11
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

Cleidy Osorio-Mogollon / Gustavo E. Olivos-Ramirez / Kewin Otazu / Manuel E. Chenet-Zuta / Georcki Ropon-Palacios / Ihosvany Camps / Gabriel M. Jimenez-Avalo / Eduardo Apari-Cossio / Natalia E. Torres-Moreira / Reyna G. Cardenas-Cardenas

2020

Abstract	The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesis of genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNA polymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drug search, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning is considered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria, which were filtered under the criteria of selecting those that do not present any violation of Lipinski's Rule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in in silico and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can be considered as drugs for the development of effective treatments against this new pandemic.
Keywords	Biochemistry ; Bioinformatics and Computational Biology ; Drug Discovery and Drug Delivery Systems ; SARS-CoV-2 ; nsp12 ; RNA polymerase binding site ; Molecular docking analysis ; drug repurposing screens ; covid19
Subject code	500
Publishing date	2020-06-19T12:38:39Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

Cleidy Osorio-Mogollon (8986702) / Gustavo E. Olivos-Ramirez (8986706) / Kewin Otazu (8961065) / Manuel E. Chenet-Zuta (8986710) / Georcki Ropon-Palacios (8986711) / Ihosvany Camps (8961050) / Gabriel M. Jimenez-Avalo (8986716) / Eduardo Apari-Cossio (8986717) / Natalia E. Torres-Moreira (8986720) / Reyna G. Cardenas-Cardenas (8986722)

2020

Abstract	The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesis of genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNA polymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drug search, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning is considered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria, which were filtered under the criteria of selecting those that do not present any violation of Lipinski's Rule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in in silico and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can be considered as drugs for the development of effective treatments against this new pandemic.
Keywords	Biochemistry ; Bioinformatics and Computational Biology ; Drug Discovery and Drug Delivery Systems ; SARS-CoV-2 ; nsp12 ; RNA polymerase binding site ; Molecular docking analysis ; drug repurposing screens ; covid19
Subject code	500
Publishing date	2020-06-19T12:38:39Z
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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