Quantum biochemistry study of the T3-785 tropocollagen triple-helical structure

Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2

Background: The RNA-dependent RNA polymerase (RdRp) complex, essential in viral transcription and replication, is a key target for antiviral therapeutics. The core unit of RdRp comprises the nonstructural protein NSP12, with NSP7 and two copies of NSP8 (NSP81 and NSP82) binding to NSP12 to enhance its affinity for viral RNA and polymerase activity. Notably, the interfaces between these subunits are highly conserved, simplifying the design of molecules that can disrupt their interaction. Methods: We conducted a detailed quantum biochemical analysis to characterize the interactions within the NSP12-NSP7, NSP12-NSP81, and NSP12-NSP82 dimers. Our objective was to ascertain the contribution of individual amino acids to these protein-protein interactions, pinpointing hotspot regions crucial for complex stability. Results: The analysis revealed that the NSP12-NSP81 complex possessed the highest total interaction energy (TIE), with 14 pairs of residues demonstrating significant energetic contributions. In contrast, the NSP12-NSP7 complex exhibited substantial interactions in 8 residue pairs, while the NSP12-NSP82 complex had only one pair showing notable interaction. The study highlighted the importance of hydrogen bonds and π-alkyl interactions in maintaining these complexes. Intriguingly, introducing the RNA sequence with Remdesivir into the complex resulted in negligible alterations in both interaction energy and geometric configuration. Conclusion: Our comprehensive analysis of the RdRp complex at the protein-protein interface provides invaluable insights into interaction dynamics and energetics. These findings can guide the design of small molecules or peptide/peptidomimetic ligands to disrupt these critical interactions, offering a strategic pathway for developing effective antiviral drugs.

Computational methods for calculation of protein-ligand binding affinities in structure-based drug design

Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.

Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry

Atrazine (ATR), one of the most used herbicides worldwide, causes persistent contamination of water and soil due to its high resistance to degradation. ATR is associated with low fertility and increased risk of prostate cancer in humans, as well as birth defects, low birth weight and premature delivery. Describing ATR binding to human serum albumin (HSA) is clinically relevant to future studies about pharmacokinetics, pharmacodynamics and toxicity of ATR, as albumin is the most abundant carrier protein in plasma and binds important small biological molecules. In this work we characterize, for the first time, the binding of ATR to HSA by using fluorescence spectroscopy and performing simulations using molecular docking, classical molecular dynamics and quantum biochemistry based on density functional theory (DFT). We determine the most likely binding sites of ATR to HSA, highlighting the fatty acid binding site FA8 (located between subdomains IA-IB-IIA and IIB-IIIA-IIIB) as the most important one, and evaluate each nearby amino acid residue contribution to the binding interactions explaining the fluorescence quenching due to ATR complexation with HSA. The stabilization of the ATR/FA8 complex was also aided by the interaction between the atrazine ring and SER454 (hydrogen bond) and LEU481(alkyl interaction).

Exploring the Spike-hACE 2 Residue-Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63

Coronaviruses (CoVs) have been responsible for three major outbreaks since the beginning of the 21st century, and the emergence of the recent COVID-19 pandemic has resulted in considerable efforts to design new therapies against coronaviruses. Thus, it is crucial to understand the structural features of their major proteins related to the virus-host interaction. Several studies have shown that from the seven known CoV human pathogens, three of them use the human Angiotensin-Converting Enzyme 2 (hACE-2) to mediate their host's cell entry: SARS-CoV-2, SARS-CoV, and HCoV-NL63. Therefore, we employed quantum biochemistry techniques within the density function theory (DFT) framework and the molecular fragmentation with conjugate caps (MFCC) approach to analyze the interactions between the hACE-2 and the spike protein-RBD of the three CoVs in order to map the hot-spot residues that form the recognition surface for these complexes and define the similarities and differences in the interaction scenario. The total interaction energy evaluated showed a good agreement with the experimental binding affinity order: SARS-2 > SARS > NL63. A detailed investigation revealed the energetically most relevant regions of hACE-2 and the spike protein for each complex, as well as the key residue-residue interactions. Our results provide valuable information to deeply understand the structural behavior and binding site characteristics that could help to develop antiviral therapeutics that inhibit protein-protein interactions between CoVs S protein and hACE-2.

Blockade of the checkpoint PD-1 by its ligand PD-L1 and the immuno-oncological drugs pembrolizumab and nivolumab

We investigate the interaction between the programmed cell death protein 1 (PD-1) and the programmed cell death ligand 1 (PD-L1), as well as the immuno-oncological drugs pembrolizumab (PEM), and nivolumab (NIV), through quantum chemistry methods based on the Density Functional Theory (DFT) and the molecular fractionation with conjugate caps (MFCC) scheme, in order to map their hot-spot regions. Our results showed that the total interaction energy order of the three complexes is in good agreement with the experimental binding affinity order: PD-1/PEM > PD-1/NIV > PD-1/PD-L1. Besides, a detailed investigation revealed the energetically most relevant residue-residue pairs-interaction for each complex. Our computational results give a better understanding of the interaction mechanism between the protein PD-1 and its ligands (natural and inhibitors), unleashing the immune surveillance to destroy the cancer cells by decreasing their immune evasion. They are also an efficient alternative towards the development of new small-molecules and antibody-based drugs, pointing out to new treatments for cancer therapy.

A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera

The worldwide dependence of population on fossil fuels continues to have several harmful implications for the environment. Bioethanol is an excellent option for renewable fuel to replace the current greenhouse gas emitters. In addition, its production by enzymatic route has gained space among the industrial processes because it replaces the traditional acid treatment. Due to its high versatility, the xylanase family is used in this process as an accessory enzyme for degrading the lignocellulosic substrate of biomass. A chimera built by a xylanolytic domain (Xyl) and a xylose-binding protein (XBP) showed an experimentally improved catalytic efficiency and interdomain allosteric modulation after xylose binding. In this context, we performed a quantum biochemistry characterization of the interactions between these domains and dynamic cross-correlation (DCC) analysis after performing molecular dynamics (DM) simulations of the systems in the presence and absence of xylose in the XBP active site. We used the density functional theory (DFT) within the molecular fractionation with the conjugated caps (MFCC) approach to describe the pair energies, and the corresponding energy difference between the chimera domains responsible for the allosteric effect and amino acid DCC to evaluate the interdomain coupling differences between the energy states. The detailed energetic investigation together with the related structural and dynamics counterparts revealed the molecular mechanisms of chimeric improvement of the xylanase activity observed experimentally. This mechanism was correlated with greater stability and high connectivity at the interdomain interface in the xylose bound relative to the free chimera. We identify the contributions of hydrogen bonds, hydrophobic interactions and water-mediated interactions in the interdomain region responsible for stability together with the structural and dynamical elements related to the allosteric effect. Taken together, these observations led to a comprehensive understanding of the chimera's modulatory action that occurs through the formation of a highly connected interface that makes the essential movements related to xylanolytic activity in xylanase correlated to those of the xylose-binding protein.

mTOR–mLST8 interaction: hot spot identification through quantum biochemistry calculations

Quantum calculation of mTOR–mLST8 interaction.

A quantum biochemistry approach to investigate checkpoint inhibitor drugs for cancer

We investigate the coupling profiles of the receptor PD-1 in complex with its natural ligand PDL1 and two inhibitor drugs.

Inhibition of the checkpoint protein PD-1 by the therapeutic antibody pembrolizumab outlined by quantum chemistry

Much of the recent excitement in the cancer immunotherapy approach has been generated by the recognition that immune checkpoint proteins, like the receptor PD-1, can be blocked by antibody-based drugs with profound effects. Promising clinical data have already been released pointing to the efficiency of the drug pembrolizumab to block the PD-1 pathway, triggering the T-lymphocytes to destroy the cancer cells. Thus, a deep understanding of this drug/receptor complex is essential for the improvement of new drugs targeting the protein PD-1. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT), we investigate in silico the binding energy features of the receptor PD-1 in complex with its drug inhibitor. Our computational results give a better understanding of the binding mechanisms, being also an efficient alternative towards the development of antibody-based drugs, pointing to new treatments for cancer therapy.

Computational investigation of the α2β1 integrin–collagen triple helix complex interaction

In this paper, quantum biochemistry methods have been used to describe important protein–protein interactions for the complex integrin–collagen.

Outlining migrainous through dihydroergotamine–serotonin receptor interactions using quantum biochemistry

We present the electronic structure of the complex dihydroergotamine–serotonin receptor to unveil new medications to treat migraine and related diseases.

Energetic description of cilengitide bound to integrin

We employ quantum chemistry methods to investigate the binding energy features of the cyclic RGD pentapeptide cilengitide interacting with the integrin receptor α_Vβ₃.

An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework

A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.

Quantum binding energy features of the T3-785 collagen-like triple-helical peptide

Structural representation of the T3-785 collagen-like triple-helical peptide depicting the 15 most and fewest energetically significant amino acids.

Explaining RANKL inhibition by OPG through quantum biochemistry computations and insights into peptide-design for the treatment of osteoporosis

Quantum biochemistry computations are applied to precisely describe important protein–protein interactions, providing a basis for the design of inhibitory peptides against osteoporosis.

A quantum chemistry investigation of a potential inhibitory drug against the dengue virus

The total interaction energy of the inhibitor Bz-nKRR-H bound to a serine protease of the dengue virus is mainly due to the action of Asn152, Met49, Tyr161, Asp129 and Gly151 (Met84, Met75, Asp81, Asp79 and Asp80) residues at the NS3 (NS2B) subunit.

Advances in skin regeneration: application of electrospun scaffolds

The paucity of cellular and molecular signals essential for normal wound healing makes severe dermatological ulcers stubborn to heal. The novel strategies of skin regenerative treatments are focused on the development of biologically responsive scaffolds accompanied by cells and multiple biomolecules resembling structural and biochemical cues of the natural extracellular matrix (ECM). Electrospun nanofibrous scaffolds provide similar architecture to the ECM leading to enhancement of cell adhesion, proliferation, migration and neo tissue formation. This Review surveys the application of biocompatible natural, synthetic and composite polymers to fabricate electrospun scaffolds as skin substitutes and wound dressings. Furthermore, the application of biomolecules and therapeutic agents in the nanofibrous scaffolds viz growth factors, genes, antibiotics, silver nanoparticles, and natural medicines with the aim of ameliorating cellular behavior, wound healing, and skin regeneration are discussed.

Quantum molecular modelling of ibuprofen bound to human serum albumin

The total interaction energies of the ibuprofen complexed with FA3/FA4 and FA6 binding sites of human serum albumin are in agreement with the hypothesis that the Sudlow's site II is the main binding pocket for ibuprofen.

Antipsychotic haloperidol binding to the human dopamine D3 receptor: beyond docking through QM/MM refinement toward the design of improved schizophrenia medicines

As the dopamine D3R receptor is a promising target for schizophrenia treatment, an improved understanding of the binding of existing antipsychotics to this receptor is crucial for the development of new potent and more selective therapeutic agents. In this work, we have used X-ray cocrystallization data of the antagonist eticlopride bound to D3R as a template to predict, through docking essays, the placement of the typical antipsychotic drug haloperidol at the D3R receptor binding site. Afterward, classical and quantum mechanics/molecular mechanics (QM/MM) computations were employed to improve the quality of the docking calculations, with the QM part of the simulations being accomplished by using the density functional theory (DFT) formalism. After docking, the calculated QM improved total interaction energy EQMDI = -170.1 kcal/mol was larger (in absolute value) than that obtained with classical molecular mechanics improved (ECLDI = -156.3 kcal/mol) and crude docking (ECRDI = -137.6 kcal/mol) procedures. The QM/MM computations reveal the pivotal role of the Asp110 amino acid residue in the D3R haloperidol binding, followed by Tyr365, Phe345, Ile183, Phe346, Tyr373, and Cys114. Besides, it highlights the relevance of the haloperidol hydroxyl group axial orientation, which interacts with the Tyr365 and Thr369 residues, enhancing its binding to dopamine receptors. Finally, our computations indicate that functional substitutions in the 4-clorophenyl and in the 4-hydroxypiperidin-1-yl fragments (such as C3H and C12H hydrogen replacement by OH or COOH) can lead to haloperidol derivatives with distinct dopamine antagonism profiles. The results of our work are a first step using in silico quantum biochemical design as means to impact the discovery of new medicines to treat schizophrenia.