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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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lima Neto, Bezerra, Barbosa, Araujo, Galvão, Lyra, Oliveira, Akash, Jardan, Nafidi, Bourhia and Fulco.)

Malaria is a parasitic disease that, in its most severe form, can even lead to death. Insect-resistant vectors, insufficiently effective vaccines, and drugs that cannot stop parasitic infestations are making the fight against the disease increasingly difficult. It is known that the enzyme dihydroorotate dehydrogenase (DHODH) is of paramount importance for the synthesis of pyrimidine from the Plasmodium precursor, that is, for its growth and reproduction. Therefore, its blockade can lead to disruption of the parasite's life cycle in the vertebrate host. In this scenario, Pf DHODH inhibitors have been considered candidates for a new therapy to stop the parasitic energy source. Given what is known, in this work, we applied molecular fractionation with conjugated caps (MFCC) in the framework of the quantum formalism of density functional theory (DFT) to evaluate the energies of the interactions between the enzyme and the different triazolopyrimidines (DSM483, DMS557, and DSM1), including a complex carrying the mutation C276F. From these results, it was possible to identify the main features of each system, focusing on the wild-type and mutant Pf DHODH and examining the major amino acid residues that are part of the four complexes. Our analysis provides new information that can be used to develop new drugs that could prove to be more effective alternatives to present antimalarial drugs.

Anabolic androgenic steroids (AAS) are substances with androgenic and anabolic characteristics. Among the many side effects of hormone therapy with AAS, the following stand out: heart problems, adrenal gland disorders, aggressive behavior, increased risk of prostate cancer, problems related to lack of libido and impotence. Such substances vary in the relationship between androgenic activity, and the activation of the androgen receptor (AR) is of fundamental importance for the singularity of the action of each AAS. In this sense, our study evaluates the aspects that comprise the interactions of testosterone agonists (TES), dihydrotestosterone (DHT) and tetrahydrogestrinone (THG) in complex with the AR. In addition, we also evaluated the impact of ligand-receptor affinity differences in a mutation model. We apply computational techniques based on density functional theory (DFT) and use, as methodology, Molecular Fractionation with Conjugate Caps (MFCC). The energetic specificities present in the interaction between the analyzed complexes attest that the highest affinity with the AR receptor is found for AR-THG, followed by AR-DHT, AR-TES and AR-T877A-DHT, respectively. Our results also show the differences and equivalences between the different agonists, in addition to evaluating the difference between the DHT ligand in complex with the wild-type and mutant receptor, presenting the main amino acid residues that involve the interaction with the ligands. The computational methodology used proves to be an operative and sophisticated choice to help in the search for pharmacological agents for various therapies that have androgen as a target.

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.

Envenomation via snakebites occurs largely in areas where it is harder to access the hospital. Its mortality rate and sequelae acquired by the survivors symbolize a big challenge for antivenom therapy. In particular, the homologous phospholipase A 2 (Lys49-PLA 2 ) proteins can induce myonecrosis and are not effectively neutralized by current treatments. Thus, by taking advantage of crystallographic structures of Bothrops moojeni Lys49-PLA 2 complexed with VRD (varespladib) and AIN (aspirin), a quantum biochemistry study based on the molecular fractionation with conjugate cap scheme within the density functional theory formalism is performed to unveil these complexes' detailed interaction energies. The calculations revealed that important interactions between ligands and the Lys49-PLA 2 pocket could occur up to a pocket radius of r = 6.5 (5.0 Å) for VRD (AIN), with the total interaction energy of the VRD ligand being higher than that of the AIN ligand, which is well-correlated with the experimental binding affinity. Furthermore, we have identified the role played by the amino acids LYS0069, LYS0049, LEU0005, ILE0009, CYS0029, GLY0030, HIS0048, PRO0018, ALA0019, CYS0045, TYR0052, TYR0022, PRO0125*, and PHE0126* (LYS0069, LYS0049, GLY0032, LEU0002, and LEU0005) in the VRD↔Lys49-PLA 2 (AIN↔Lys49-PLA 2 ) complex. Our simulations are a valuable tool to support the big challenge for neutralizing the damages in victims of snakebites.

Ethionamide (ETH) is a high-profile drug for the treatment of patients with multidrug-resistant Mycobacterium tuberculosis and, in order to produce its inhibitory effects, it needs to be bioactivated by monooxygenase EthA. This process is under the control of the transcriptional repressors EthR and EthR2, so that their inhibition results in the boosting of ethionamide activation. Herein, through crystallographic data and computer simulations, we calculated the interaction binding energies of four inhibitors with improved in vitro potency, namely BDM76060 (PDB ID: 6HS1), BDM72201 (PDB ID: 6HRX), BDM76150 (PDB ID: 6HS2) and BDM72719 (PDB ID: 6HRY), in complexes with the transcriptional repressor EthR2, using density functional theory (DFT) within the molecular fractionation with conjugated caps (MFCC) approach. It was observed that these ligands share the same binding site within a 10.0 Å radius of the EthR2 protein; however, their structural particularities have a significant impact on the global energies of systems. The BDM72201 and BDM72719 components are weakly attached to the binding site, while BDM76060 and BDM76150 components produce stronger bonds, corroborating with experimental studies demonstrating that BDM76060 and BDM76150 are more successful in producing inhibitory effects. BDM76060 and BDM76150 have many functional groups that increase the contact surface with the protein and attract a more significant number of amino acid residues, being able to produce polarities that generate stronger interactions. In the current scenario of a growing number of cases of bacterial resistance, the obtained data can be used to guide clinical trials of these inhibitors and other inhibitors that act on the alternative EthR2 pathway, focusing on improving the activity of ethionamide, its effectiveness, a reduction in the treatment time and exposure to cytotoxic effects.

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.

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.

GABA B is a G protein-coupled receptor that functions as a constitutive heterodimer composed of the GABA B1a/b and GABA B2 subunits. It mediates slow and prolonged inhibitory neurotransmission in the nervous system, representing an attractive target for the treatment of various disorders. However, the molecular mechanism of the GABA B receptor is not thoroughly understood. Therefore, a better description of the binding of existing agonists and antagonists to this receptor is crucial to improve our knowledge about G protein-coupled receptor structure as well as for helping the development of new potent and more selective therapeutic agents. In this work, we used the recent X-ray cocrystallization data of agonists (GABA and baclofen) and antagonists (2-hydroxysaclofen, SCH50911, and CGP54626) bound to the GABA B orthosteric site together with quantum biochemistry and the molecular fractionation with conjugate caps (MFCC) scheme to describe the individual contribution of each amino acid residue involved in the GABA B -ligand interaction, pointing out differences and similarities among the compounds. Our quantum biochemical computational results show that the total binding energy of the ligands to the GABA B ligand pocket, with radius varying from 2.0 to 9.0 Å, is well-correlated with the experimental binding affinity. In addition, we found that the binding site is very similar for agonists or antagonists, showing small differences in the importance of the most significant amino acids. Finally, we predict the energetic relevance of the regions of the five ligands as well as the influence of each protein lobe on GABA B -ligand binding. These results provide important new information on the binding mechanism of the GABA B receptor and should facilitate the development of new chemicals targeting this receptor.

We intend to investigate the drug-binding energy of each nucleotide inside the aminoglycoside hygromycin B (hygB) binding site of 30S ribosomal RNA (rRNA) subunit by using the molecular fractionation with conjugate caps (MFCC) strategy based on the density functional theory (DFT), considering the functional LDA/PWC, OBS, and the dielectric constant parametrization. Aminoglycosides are bactericidal antibiotics that have high affinity to the prokaryotic rRNA, inhibiting the synthesis of proteins by acting on the main stages of the translation mechanism, whereas binding to rRNA 16S, a component of the 30S ribosomal subunit in prokaryotes. The identification of the nucleotides presenting the most negative binding energies allows us to stabilize hygB in a suitable binding pocket of the 30S ribosomal subunit. In addition, it should be highlighted that mutations in these residues may probably lead to resistance to ribosome-targeting antibiotics. Quantum calculations of aminoglycoside hygromycin B-ribosome complex might contribute to further quantum studies with antibiotics like macrolides and other aminoglycosides.

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.

We employ quantum biochemistry methods based on the Density Functional Theory (DFT) approach to unveil the detailed binding energy features of willardiines co-crystallized with the AMPA receptor. Our computational results demonstrate that the total binding energies of fluorine-willardiine (FW), hydrogen-willardiine (HW), bromine-willardiine (BrW) and iodine-willardiine (IW) to the iGluR2 ligand-pocket correlate with the agonist binding energies, whose experimental sequential data match our computational counterpart, excluding the HW case. We find that the main contributions to the total willardiine-iGluR2 binding energy are due to the amino acid residues in decreasing order Glu705 > Arg485 > Ser654 > Tyr450 > T655. Furthermore, Met708, which is positioned close to the 5-substituent, attracts HW and FW, but repels BrW and IW. Our results contribute significantly to an improved understanding of the willardiine-iGluR2 binding mechanisms.