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Article ; Online: Evaluation of structural and thermodynamic insight of ERβ with DPN and derivatives through MMGBSA/MMPBSA methods.

Bello, Martiniano

2023 Volume 201, Page(s) 109334

Abstract: Estrogen receptors (ERs) are nuclear factors that exist as two subtypes: ERα and ERβ. Among the different selective ERβ agonist ligands, the widely used ERβ-selective agonist DPN (diarylpropionitrile) is highlighted. Recent experimental and thermodynamic ...

Abstract	Estrogen receptors (ERs) are nuclear factors that exist as two subtypes: ERα and ERβ. Among the different selective ERβ agonist ligands, the widely used ERβ-selective agonist DPN (diarylpropionitrile) is highlighted. Recent experimental and thermodynamic information between R-DPN and S-DPN enantiomers with ERβ is important for evaluating further the ability of MD simulations combined with end-point methods to reproduce experimental binding affinity and generate structural insight not provided through crystallographic data. In this research, starting from crystallographic data and experimental binding affinities, we explored the structural and thermodynamic basis of the molecular recognition of ERβ with DPN and derivatives through triplicate MD simulations combined with end-point methods. Conformational analysis showed some regions with the highest mobility linked to ligand association that, at the time, impacted the total protein fluctuation. Binding free energy (ΔG) analysis revealed that the Molecular Mechanics Generalized-Born Surface Area (MMGBSA) approach was able to reproduce the experimental tendency with a strong correlation (R = 0.778), whereas per-residue decomposition analysis revealed that all the systems interacted strongly with eight residues (L298, E305, L339, M340, L343, F356, H475, and L476). The comparison between theoretical studies using the MMGBSA approach with experimental results provides new insights for drug designing of new DPN derivatives.
MeSH term(s)	Estrogen Receptor beta/metabolism ; Receptors, Estrogen/metabolism ; Estrogen Receptor alpha/metabolism ; Ligands ; Molecular Conformation ; Thermodynamics ; Nitriles/chemistry ; Estradiol
Chemical Substances	Estrogen Receptor beta ; Receptors, Estrogen ; Estrogen Receptor alpha ; Ligands ; Nitriles ; Estradiol (4TI98Z838E)
Language	English
Publishing date	2023-11-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	80312-1
ISSN	1878-5867 ; 0039-128X
ISSN (online)	1878-5867
ISSN	0039-128X
DOI	10.1016/j.steroids.2023.109334
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Article ; Online: Molecular recognition of tak-285 and lapatinib by inactive, active, and middle active-inactive HER2.

Martiniano, Bello

Journal of molecular modeling

2021 Volume 27, Issue 4, Page(s) 105

Abstract: Experimental and theoretical studies have provided structural information regarding the shift from inactive to active EGFR, throughout which both conformations are linked via binding to specific tyrosine kinase inhibitors. For HER2, an intermediate ... ...

Abstract	Experimental and theoretical studies have provided structural information regarding the shift from inactive to active EGFR, throughout which both conformations are linked via binding to specific tyrosine kinase inhibitors. For HER2, an intermediate active-inactive receptor conformation is present in the PDB, which has been co-crystallized with tak-285. The affinity of HER2 in monomeric state to tak-285 has been previously reported. However, the lack of structural knowledge of HER2 limits our capacity to understand whether tak-285, or other known HER2 inhibitors, selectively bind active, inactive, or intermediate forms of HER2. To elucidate mechanisms by which tak-285 binds to HER2, we first obtained information regarding the structural features of the active state of HER2 via microsecond MD simulations from the crystallized intermediate structure previously determined. Based on these HER2 conformers, together with the inactive HER2 conformer obtained in a previous study, we used docking and MD simulations coupled to MMGBSA approach to assess binding of tak-285 and lapatinib, known HER2/EGFR dual inhibitors, to HER2. Structural and energetic studies revealed that tak-285 binds with a greater affinity than lapatinib to active and intermediate active-inactive forms of HER2. This is in accordance with experimental findings that showed the tak-285 inhibitor has increased activity relative to lapatinib in breast cancer cell lines.
MeSH term(s)	Antineoplastic Agents/chemistry ; Bridged Bicyclo Compounds, Heterocyclic/chemistry ; Humans ; Hydroxybutyrates/chemistry ; Lapatinib/chemistry ; Models, Molecular ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Receptor, ErbB-2/chemistry
Chemical Substances	Antineoplastic Agents ; Bridged Bicyclo Compounds, Heterocyclic ; Hydroxybutyrates ; Lapatinib (0VUA21238F) ; N-(2-(4-((3-chloro-4-(3-(trifluoromethyl)phenoxy)phenyl)amino)-5H-pyrrolo(3,2-d)pyrimidin-5-yl)ethyl)-3-hydroxy-3-methylbutanamide (70CCB438L6) ; ERBB2 protein, human (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2021-03-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-021-04720-5
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Article ; Online: Molecular Basis of Inhibitory Mechanism of Naltrexone and Its Metabolites through Structural and Energetic Analyses

Martiniano Bello

Molecules, Vol 27, Iss 4919, p

2022 Volume 4919

Abstract: Naltrexone is a potent opioid antagonist with good blood–brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against ... ...

Abstract	Naltrexone is a potent opioid antagonist with good blood–brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of naltrexone and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. Naltrexone and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to the molecular mechanics–generalized Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that naltrexone and its derivatives showed differences in protein–ligand interactions; however, they shared contacts with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of naltrexone compared to its derivatives.
Keywords	naltrexone ; mu-opioid receptor ; MD simulations ; MMGBSA ; binding free energy ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Molecular Basis of Inhibitory Mechanism of Naltrexone and Its Metabolites through Structural and Energetic Analyses.

Bello, Martiniano

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 15

Abstract: Naltrexone is a potent opioid antagonist with good blood-brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against ... ...

Abstract	Naltrexone is a potent opioid antagonist with good blood-brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of naltrexone and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. Naltrexone and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to the molecular mechanics-generalized Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that naltrexone and its derivatives showed differences in protein-ligand interactions; however, they shared contacts with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of naltrexone compared to its derivatives.
MeSH term(s)	Animals ; Humans ; Ligands ; Mice ; Molecular Dynamics Simulation ; Naltrexone/pharmacology ; Narcotic Antagonists/pharmacology ; Receptors, Opioid, mu/metabolism ; Water
Chemical Substances	Ligands ; Narcotic Antagonists ; Receptors, Opioid, mu ; Water (059QF0KO0R) ; Naltrexone (5S6W795CQM)
Language	English
Publishing date	2022-08-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27154919
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Article ; Online: Structural basis of Nrf2 activation by flavonolignans from silymarin.

Bello, Martiniano

Journal of molecular graphics & modelling

2022 Volume 119, Page(s) 108393

Abstract: Several properties of silymarin (SM) extract have been attributed to their three major flavonolignans (silybin, silychristin, and silydianin) and their 2,3-dehydro derivatives (2,3-dehydrosilybin, 2,3-dehydrosilychristin, and 2,3-dehydrosilydianin). ... ...

Abstract	Several properties of silymarin (SM) extract have been attributed to their three major flavonolignans (silybin, silychristin, and silydianin) and their 2,3-dehydro derivatives (2,3-dehydrosilybin, 2,3-dehydrosilychristin, and 2,3-dehydrosilydianin). Experimental findings have suggested that the antioxidative and protective activities of these compounds could be due to their ability to activate nuclear factor erythroid 2-related factor 2 (Nrf2). The mechanism by which SM compounds exert their effect has been suggested to be by disrupting the complex between Nrf2 and Kelch-like ECH-associated protein 1 (Keap1). However, information about the structural and energetic basis of the inhibitory mechanism of SM compounds on the Nrf2-Keap1 pathway is lacking. We evaluated the binding properties of SM compounds because experimental findings have pointed to them as potential activators of Nrf2. Our study combined docking and molecular dynamics (MD) simulations with the Poisson-Boltzmann and generalized Born and surface area (MMPBSA and MMGBSA) methods and quantum mechanics-molecular mechanics (QMMM) calculations to investigate Keap1-ligand interactions. Our results predicted that silybin
MeSH term(s)	Silybin ; Kelch-Like ECH-Associated Protein 1/chemistry ; Kelch-Like ECH-Associated Protein 1/metabolism ; NF-E2-Related Factor 2/metabolism ; Silymarin/pharmacology ; Silymarin/chemistry ; Antioxidants/pharmacology ; Antioxidants/chemistry
Chemical Substances	Silybin (4RKY41TBTF) ; Kelch-Like ECH-Associated Protein 1 ; NF-E2-Related Factor 2 ; Silymarin ; Antioxidants
Language	English
Publishing date	2022-12-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2022.108393
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Article ; Online: Evaluation of

Culhuac, Erick Bahena / Bello, Martiniano

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 8

Abstract: Allergic rhinitis (AR) is a prevalent inflammatory condition affecting millions globally, with current treatments often associated with significant side effects. To seek safer and more effective alternatives, natural sources ... ...

Abstract	Allergic rhinitis (AR) is a prevalent inflammatory condition affecting millions globally, with current treatments often associated with significant side effects. To seek safer and more effective alternatives, natural sources like
MeSH term(s)	Phytochemicals/chemistry ; Phytochemicals/pharmacology ; Phytochemicals/therapeutic use ; Molecular Docking Simulation ; Rhinitis, Allergic/drug therapy ; Molecular Dynamics Simulation ; Humans ; Urtica dioica/chemistry ; Plant Extracts/chemistry ; Plant Extracts/pharmacology
Chemical Substances	Phytochemicals ; Plant Extracts
Language	English
Publishing date	2024-04-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules29081765
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Article ; Online: Elucidation of the inhibitory activity of ivermectin with host nuclear importin α and several SARS-CoV-2 targets.

Bello, Martiniano

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 18, Page(s) 8375–8383

Abstract: Ivermectin (IVM) is an FDA-approved drug that has shown antiviral activity against a wide variety of viruses in recent years. IVM inhibits the formation of the importin-α/β1 heterodimeric complex responsible for the translocation and replication of ... ...

Abstract	Ivermectin (IVM) is an FDA-approved drug that has shown antiviral activity against a wide variety of viruses in recent years. IVM inhibits the formation of the importin-α/β1 heterodimeric complex responsible for the translocation and replication of various viral species proteins. Also, IVM hampers SARS-CoV-2 replication in vitro; however, the molecular mechanism through which IVM inhibits SARS-CoV-2 is not well understood. Previous studies have explored the molecular mechanism through which IVM inhibits importin-α and several potential targets associated with COVID-19 by using docking approaches and MD simulations to corroborate the docked complexes. This study explores the energetic and structural properties through which IVM inhibits importin-α and five targets associated with COVID-19 by using docking and MD simulations combined with the molecular mechanics generalized Born surface area (MMGBSA) approach. Energetic and structural analysis showed that the main protease 3CL
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Ivermectin/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases/metabolism ; Protease Inhibitors/chemistry ; SARS-CoV-2 ; Viral Proteins ; alpha Karyopherins
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Viral Proteins ; alpha Karyopherins ; Ivermectin (70288-86-7) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-04-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1911857
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Article ; Online: Evaluating the ability of end-point methods to predict the binding affinity tendency of protein kinase inhibitors.

Bello, Martiniano / Bandala, Cindy

RSC advances

2023 Volume 13, Issue 36, Page(s) 25118–25128

Abstract: Because of the high economic cost of exploring the experimental impact of mutations occurring in kinase proteins, computational approaches have been employed as alternative methods for evaluating the structural and energetic aspects of kinase mutations. ... ...

Abstract	Because of the high economic cost of exploring the experimental impact of mutations occurring in kinase proteins, computational approaches have been employed as alternative methods for evaluating the structural and energetic aspects of kinase mutations. Among the main computational methods used to explore the affinity linked to kinase mutations are docking procedures and molecular dynamics (MD) simulations combined with end-point methods or alchemical methods. Although it is known that end-point methods are not able to reproduce experimental binding free energy (Δ
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d3ra04916g
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Article ; Online: Prediction of potential inhibitors of the dimeric SARS-CoV2 main proteinase through the MM/GBSA approach.

Bello, Martiniano

Journal of molecular graphics & modelling

2020 Volume 101, Page(s) 107762

Abstract: Since the emergence of SARS-CoV2, to date, no effective antiviral drug has been approved to treat the disease, and no vaccine against SARS-CoV2 is available. Under this scenario, the combination of two HIV-1 protease inhibitors, lopinavir and ritonavir, ... ...

Abstract	Since the emergence of SARS-CoV2, to date, no effective antiviral drug has been approved to treat the disease, and no vaccine against SARS-CoV2 is available. Under this scenario, the combination of two HIV-1 protease inhibitors, lopinavir and ritonavir, has attracted attention since they have been previously employed against the SARS-CoV main proteinase (M
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Coronavirus 3C Proteases ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/metabolism ; Lopinavir/chemistry ; Lopinavir/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Principal Component Analysis ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protein Conformation ; Protein Multimerization ; Ritonavir/chemistry ; Ritonavir/pharmacology ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Viral Nonstructural Proteins ; Lopinavir (2494G1JF75) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Ritonavir (O3J8G9O825)
Keywords	covid19
Language	English
Publishing date	2020-09-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2020.107762
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Article ; Online: Structural mechanism of the Tanford transition of bovine β-lactoglobulin through microsecond molecular dynamics simulations.

Bello, Martiniano

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 7, Page(s) 3011–3023

Abstract: X-ray analysis has provided structural data about a pH-driven conformational change in β-lactoglobulin (BLG) known as the Tanford transition, which occurs at around pH 7 and involves the EF loop, which acts as a lid closing the internal cavity of the ... ...

Abstract	X-ray analysis has provided structural data about a pH-driven conformational change in β-lactoglobulin (BLG) known as the Tanford transition, which occurs at around pH 7 and involves the EF loop, which acts as a lid closing the internal cavity of the protein below pH 7 and opening it above pH 7. NMR studies using wild-type BLG have encountered problems trying to explain the Tanford transition, however, they have provided important insight using a dimeric BLG mutant, revealing that the opening and closure of the EF loop consists of two types of motions in the microsecond and milliseconds timescales. This provides valuable information indicating that the dimeric state is a good model to study the Tanford transition, although the understanding of this structural change is still lacking at the atomic level. We performed microsecond molecular dynamics (MD) simulations starting from different conformations of BLG in the monomeric and dimeric state, with protonated and deprotonated E89, in order to explore the Tanford transition. Our results provide structural information for the transition from the closed to the open conformation in BLG and show it occurs in the dimeric state in the microsecond timescale, in line with the fast motion observed through NMR experiments. In addition, MD simulations coupled to MMGBSA approach indicated that the most populated conformer of BLG in the open state is able to bind ligands with similar affinity to that of BLG at neutral pH obtained through crystallographic experiments.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Animals ; Cattle ; Hydrogen-Ion Concentration ; Lactoglobulins/chemistry ; Ligands ; Magnetic Resonance Spectroscopy ; Molecular Dynamics Simulation ; Protein Conformation
Chemical Substances	Lactoglobulins ; Ligands
Language	English
Publishing date	2020-11-06
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1844062
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