Pharmacophore Based Screening & Modification of Amiloride Analogs for Targeting the NhaP-type Cation-Proton Antiporter in Vibrio cholerae

The genome of Vibrio cholerae contains three structural genes for the NhaP-type cation-proton antiporter paralogues, Vc-NhaP1, 2 and 3 mediating exchange of K+ and or Na+ for protons across the membrane. Based on phenotype analysis of chromosomal Vc-NhaP1, 2 and 3 triple deletion mutants we suggested that Vc-NhaP paralogues might play a role in the Acid Tolerance Response (ATR) of V. cholerae as it passes through the gastric acid barrier of the stomach. Comparison of the biochemical properties of Vc-NhaP isoforms revealed that Vc-NhaP2 is the most active among all three paralogues. Therefore, Vc-NhaP2 antiporter is a plausible therapeutic target for developing novel inhibitors targeting these ion exchangers. Our structural and mutational analysis of Vc-NhaP2 identified a putative cation binding pocket formed by antiparallel extended regions of two transmembrane segments (TMSs V/XII) along with TMS VI. Molecular Dynamics (MD) simulations suggested that the flexibility of TMS-V/XII is crucial for the intra-molecular conformational events in Vc-NhaP2. In this study, we developed some putative Vc-NhaP2 inhibitors from Amiloride analogs (AAs). Amiloride is a potent inhibitor of human Na+/H+ exchanger-1 (NHE1). Based on the pharmacokinetic properties and potential binding affinity scores we chose six AAs showing high binding affinity scores to Vc-NhaP2. In silico, the six AAs interacted with the functionally important amino acid residues located in TMSs III, IV, V, VI, VIIII and IX either from the cytoplasmic side (three AAs) or the periplasmic side (three AAs) of Vc-NhaP2. Four AAs were modified to reduce their toxicity profile compared to the original AAs. Molecular docking of the modified AAs revealed promising binding. The four selected drugs interacted with functionally important amino acid residues located on the cytoplasmic side of TMS VI, the extended chain region of TMS V and TMS XII and the loop region between TMSs VIIII and IX. Molecular dynamics simulations revealed that binding of the selected drugs destabilized the Vc-NhaP2 and altered the flexibility of functionally important TMS VI.

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Pharmacophore-Based Screening & Modification of Amiloride Analogs for targeting the NhaP-type Cation-Proton Antiporter in Vibrio cholerae

Canadian Journal of Microbiology ◽

10.1139/cjm-2021-0074 ◽

2021 ◽

Author(s):

Muntahi Mourin ◽

Arittra Bhattacharjee ◽

Alvan Wai ◽

Georg Hausner ◽

Joe O'Neil ◽

...

Keyword(s):

Molecular Dynamics ◽

Vibrio Cholerae ◽

Mutational Analysis ◽

Md Simulations ◽

Binding Pocket ◽

Cation Binding ◽

Important Amino Acid ◽

Loop Region ◽

Dynamics Simulations ◽

Amiloride Analogs

Structural and mutational analysis of Vc-NhaP2 identified a putative cation binding pocket formed by antiparallel extended regions of two transmembrane segments (TMSs V/XII) along with TMS VI. Molecular Dynamics (MD) simulations suggested that the flexibility of TMS-V/XII is crucial for the intra-molecular conformational events in Vc-NhaP2. In this study, we developed some putative Vc-NhaP2 inhibitors from Amiloride analogs (AAs). Molecular docking of the modified AAs revealed promising binding. The four selected drugs potentially interacted with functionally important amino acid residues located on the cytoplasmic side of TMS VI, the extended chain region of TMS V and TMS XII and the loop region between TMSs VIIII and IX. Molecular dynamics simulations revealed that binding of the selected drugs can potentially destabilize the Vc-NhaP2 and alters the flexibility of the functionally important TMS VI. The work presents the utility of in silico approaches for the rational identification of potential targets and drugs that could target NhaP2 cation proton antiporter to control Vibrio cholerae. The goal is to identify potential drugs that can be validated in future experiments.

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Structural Insights Into the Design of Peptide-based Drug or Diagnostic Reagent Antagonizing SARS-COV-2

10.21203/rs.3.rs-45305/v1 ◽

2020 ◽

Author(s):

junhao jiang ◽

Ping Deng

Keyword(s):

Amino Acid ◽

Binding Affinity ◽

Great Promise ◽

Amino Acid Residues ◽

Important Amino Acid ◽

Amino Acid Mutations ◽

Α Helix ◽

New Interactions ◽

Structural Insights ◽

Blocking Capacity

Abstract Background Very limited drug and diagnostic reagents are currently available to tackle the emergence of SARS-CoV-2. However, recent findings about the structure of the complex about PD of ACE2 and RBD of SARS-CoV-2 spike protein hold great promise for the design of novel vaccines and peptides. To provide some suggestions for the design of peptide-based drug or diagnostic reagents antagonizing SARS-CoV-2, and describe the interactions between the receptor-binding domain of SARS-CoV-2 and PD domain of its receptor, ACE2. Methods Based on the PD-RBD crystal structure, the molecular interaction details of PD-RBD was contrasted. Results Amino acid mutations located in RBM of SARS-CoV result in the formation of new interactions between SARS-CoV-2 and α-helix 1, which can increase the binding affinity of SARS-CoV-2 to ACE2. It is confirmed that the α-helix 1 on ACE2 is the most important domain for binding spike glycoprotein of SARS-CoV-2, which can be used as a leading peptide for drug and diagnostic reagents development. Conclusion Based on the molecular-level characterization analysis between the PD and RBD, severe important amino acid residues (Q24, T27, K31, and H34) on α-helix 1 are proposed to mutate into increasing the binding affinity. Although the information provided in this study is predictive and based on no experimental evidence, it may provide useful suggestions for the experimental scientists to synthesize the proposed peptide and test their binding affinity and blocking capacity, and may be helpful for the understanding of SARS-CoV-2 entry.

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Molecular Dynamics Analysis of Glucose Oxidase Stability against Temperature

Biointerface Research in Applied Chemistry ◽

10.33263/briac123.40624073 ◽

2021 ◽

Vol 12 (3) ◽

pp. 4062-4073

Keyword(s):

Molecular Dynamics ◽

Thermal Stability ◽

Amino Acid ◽

Glucose Oxidase ◽

Dynamics Simulation ◽

Amino Acid Residues ◽

Widespread Application ◽

Important Amino Acid ◽

Ribose Sugar ◽

Fad Binding

Glucose oxidase (GOD) from local isolated Aspergillus niger IPBCC.08.610 shows a widespread application, specifically as a bioanode in glucose-based biofuel cells. Enzymes with adequate thermal stability are necessary for enhancing product efficiency. Also, evaluating the structural dynamics to improve temperature helps to determine the residue. The molecular dynamics simulation of GOD_IPBCC_1CF3 at temperatures of 300, 400, and 500 K was carried out to analyze important amino acid residues for thermal stability. The results showed that the amino acid residues responsible for thermal stability were dispersed into several essential regions, including D576 at the C terminal, E266-R250, and E38-R237 in the FAD-binding domain E485-R470 in the substrate-binding antiparallel beta system. However, the FAD molecular flexibility against temperature depends on conserve E48 by stabilizing the ribose sugar moiety.

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Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

Current Computer - Aided Drug Design ◽

10.2174/1573409915666190708103132 ◽

2020 ◽

Vol 16 (4) ◽

pp. 451-459 ◽

Cited By ~ 1

Author(s):

Fortunatus C. Ezebuo ◽

Ikemefuna C. Uzochukwu

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Binding Energy ◽

Binding Site ◽

Conformational Dynamics ◽

Side Chain ◽

Amino Acid Residues ◽

Conformational Selection ◽

Hybrid Mechanism ◽

Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

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New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽

10.1039/c4ra09897h ◽

2014 ◽

Vol 4 (89) ◽

pp. 48621-48631 ◽

Cited By ~ 9

Author(s):

Eleanor R. Turpin ◽

Sam Mulholland ◽

Andrew M. Teale ◽

Boyan B. Bonev ◽

Jonathan D. Hirst

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Amino Acid Residues ◽

Charmm Force Field ◽

Force Field Parameters ◽

Dynamics Simulations

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Important Amino Acid Residues that Confer CYP2C19 Selective Activity to CYP2C9

The Journal of Biochemistry ◽

10.1093/jb/mvn070 ◽

2008 ◽

Vol 144 (3) ◽

pp. 323-333 ◽

Cited By ~ 14

Author(s):

Y. Wada ◽

M. Mitsuda ◽

Y. Ishihara ◽

M. Watanabe ◽

M. Iwasaki ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Residues ◽

Important Amino Acid ◽

Selective Activity

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ReaxFF-based molecular dynamics simulation of the interaction between plasma ROS and the receptor-binding domain of the spike protein in the capsid protein of SARS-CoV-2

Journal of Physics D Applied Physics ◽

10.1088/1361-6463/ac360e ◽

2021 ◽

Author(s):

Huichao Wang ◽

Tong Zhao ◽

Shuhui Yang ◽

Liang Zou ◽

Xiaolong Wang ◽

...

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Capsid Protein ◽

Receptor Binding ◽

Hydrogen Abstraction ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Amino Acid Residues ◽

Global Epidemic

Abstract Under the severe situation of the current global epidemic, researchers have been working hard to find a reliable way to suppress the infection of the virus and prevent the spread of the epidemic. Studies have shown that the recognition and binding of human angiotensin-converting enzyme 2 (ACE2) by the receptor-binding domain (BRD) of spike protein on the surface of SARS-CoV-2 is a crucial step for SARS-CoV-2 to invade human receptor cells, and blocking this process can inhibit the virus from invading human normal cells. Plasma treatment can disrupt the structure of the RBD and effectively block the binding process. However, the mechanism by which plasma blocks the recognition and binding between the two is not clear. In this study, reaction process between reactive oxygen species (ROS) in plasma and the molecular model of RBD was simulated using a reactive molecular dynamics method. The results showed that the destruction of RBD molecule by ROS was triggered by hydrogen abstraction reactions. O and OH abstracted H atoms from RBD, while the H atoms of H2O2 and HO2 were abstracted by RBD. The hydrogen abstraction resulted in the breakage of C-H, N-H, O-H and C=O bonds and the formation of C=C, C=N bonds. The addition reaction of OH increased the number of O-H bonds and caused the formation of C-O, N-O and O-H bonds. The dissociation of N-H bonds led to the destruction of the original structure of peptide bonds and amino acid residues, change the type of amino acid residues, and caused the conversion of N-C and N=C, C=O and C-O. The simulation partially elucidated the microscopic mechanism of the interaction between ROS in plasma and the capsid protein of SARS-CoV-2, providing theoretical support for the control of SARS-CoV-2 infection by plasma, a contribution to overcoming the global epidemic problem.

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SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

SLAS DISCOVERY Advancing Life Sciences ◽

10.1177/2472555219867317 ◽

2019 ◽

Vol 24 (9) ◽

pp. 928-938 ◽

Cited By ~ 4

Author(s):

Luca Palazzolo ◽

Chiara Paravicini ◽

Tommaso Laurenzi ◽

Sara Adobati ◽

Simona Saporiti ◽

...

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Amino Acid ◽

Molecular Dynamics Simulations ◽

Electrostatic Interactions ◽

Amino Acid Residues ◽

Dibasic Amino Acid ◽

Novel Target ◽

Function Relationship ◽

Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

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Plural Origins of Molecular Homochirality in Our Biota Part II. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides

Zeitschrift für Naturforschung C ◽

10.1515/znc-1997-1-216 ◽

1997 ◽

Vol 52 (1-2) ◽

pp. 89-96 ◽

Cited By ~ 6

Author(s):

Thereza Amélia Soares ◽

Roberto Dias Lins ◽

Ricardo Longo ◽

Richard Garratt ◽

Ricardo Ferreira

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Force Field ◽

Molecular Mechanics ◽

Computer Simulations ◽

The Other ◽

Amino Acid Residues ◽

Relative Stabilities ◽

Amber Force Field ◽

Cross Inhibition

Abstract By computer simulations -molecular mechanics and molecular dynamics with the amber force field (Weiner et al., (1986), J. Comp. Chem. 7, 2 30-252) -we have determined the stabilities of oligoribotide strands built with ᴅ -and ʟ-riboses, and of peptide chains with ᴅ -and ʟ-amino acid residues. In particular, complementary double-chains of oligoribotides were studied, since they are an important feature of the growing mechanism of modern nucleic acids. Peptide chains on the other hand, grow without need of a template. We found that mixed oligoribotides are less stable than homochiral ones, and that this chiral effect is less noticeable in peptide chains. The results support the interpretation that ʟ-riboses act as terminators to the template-assisted growth of oligo-r-Gᴅ (enantiomeric cross-inhibition; Joyce et al., (1987), Proc. Natl. Acad. Sci. USA 84, 4398-4402). Based on this effect, a chemical pathway is proposed which could, under assumed prebiotic conditions, bypass the hindrance of homochiral growth.

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