Computer-assisted design of new drugs based on retrometabolic concepts

SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics

Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values ​​for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.

Retrometabolic drug design: Principles and recent developments

Retrometabolic drug design incorporates two major systematic approaches: the design of soft drugs (SDs) and of chemical delivery systems (CDSs). Both aim to design new, safe drugs with an improved therapeutic index by integrating structure-activity and -metabolism relationships; however, they achieve it by different means: whereas SDs are new, active therapeutic agents that undergo predictable metabolism to inactive metabolites after exerting their desired therapeutic effect, CDSs are biologically inert molecules that provide enhanced and targeted delivery of an active drug to a particular organ or site through a designed sequential metabolism that involves several steps. General principles and recent developments are briefly reviewed with various illustrative examples from different therapeutic areas with special focus on soft corticosteroids and on brain targeting.

General Linearized Biexponential Model for QSAR Data Showing Bilinear-Type Distribution

A major impediment of many QSAR-type analyses is that the data show a maximum or minimum and can no longer be adequately described by linear functions that provide unrivaled simplicity and usually give good description over more restricted ranges. Here, a general linearized biexponential (LinBiExp) model is proposed that can adequately describe data showing bilinear-type distribution as a function of not just often-employed lipophilicity descriptors (e.g., log P) but as a function of any descriptor (e.g., molecular volume). Contrary to Hansch-type parabolic models, LinBiExp allows the natural extension of linear models and fitting of asymmetrical data. It is also more general and intuitive than Kubinyi's model as it has a more natural functional form. It was obtained by a differential equation-based approach starting from very general assumptions that cover both static equilibria and first-order kinetic processes and that involve abstract processes through which the concentration of the compound of interest in an assumed "effect" compartment is connected to its "external" concentration. Physicochemical aspects placing LinBiExp within the framework of linear free energy relationship (LFER) approaches are presented together with illustrative applications in various fields such as toxicity, antimicrobial activity, anticholinergic activity, and glucocorticoid receptor binding.

Attempts of ranking in a series of synthetic nonpsychotropic cannabinoids

Dexanabinol and other synthetic 6aS-trans cannabinoids are devoid of cannabimimetic activity, as they do not have affinity toward cannabinoid receptors. On the other hand, these compound bind to the NMDA receptor and possess neuroprotective properties. A ranking of 6aS-trans cannabinoids based on their NMDA receptor binding affinity and by using a variety of calculated properties included in a fully computerized expert system has been attempted. The results of the study indicate that either the present isosteric-isoelectronic-based ranking criteria is not adequate to reproduce NMDA receptor binding or that some other members of the series rather than dexanabinol are the true lead compounds of 6aS-trans cannabinoids.

Capecitabine

Drug development has undergone rapid shifts in methodology and the use of rationally derived agents which either target specific tissues or molecules such as receptors or enzymatic sites. Capecitabine is a rationally derived prodrug of 5-fluorouracil which is based upon the known high concentration of the enzyme thymidine phosphorylase in many human tumors. The first prodrug designed to exploit this biochemical finding was 5-DFUR which allowed cytotoxic 5-fluorouracil to be preferentially concentrated in tumors. Unfortunately, in man this agent was associated with significant gastrointestinal toxicity. Further manipulation of this molecular resulted in capecitabine which is a relatively inert prodrug, undergoes three enzymatic steps, and offers the potential of less gastrointestinal toxicity. Phase I trials have examined several schedules with the divided oral daily x 14 schedule every 3 weeks as the preferred phase II and phase III dosing method. This agent demonstrates significant antitumor effect in diseases known to be responsive to fluoropyrimidines. Further study is needed to determine whether capecitabine has a broader spectrum of action thus affecting other tumor types than 5-fluorouracil. Major dose limiting toxicities have been hand foot syndrome, nausea/vomiting, and diarrhea.

Soft drug design: general principles and recent applications

Soft drug design represents a new approach aimed to design safer drugs with an increased therapeutic index by integrating metabolism considerations into the drug design process. Soft drugs are new therapeutic agents that undergo predictable metabolism to inactive metabolites after exerting their therapeutic effect. Hence, they are obtained by building into the molecule, in addition to the activity, the most desired way in which the molecule is to be deactivated and detoxified. In an attempt to systematize and summarize the related work done in a number of laboratories, including ours, the present review presents an overview of the general soft drug design principles and provides a variety of specific examples to illustrate the concepts. A number of already marketed drugs, such as esmolol, remifentanil, or loteprednol etabonate, resulted from the successful application of such design principles. Many other promising drug candidates are currently under investigation in a variety of fields including possible soft antimicrobials, anticholinergics, corticosteroids, beta-blockers, analgetics, ACE inhibitors, antiarrhythmics, and others. Whenever possible, pharmacokinetic and pharmacodynamic properties are briefly summarized and compared to those of other compounds used in the same field.

Quantitative structure-metabolism relationships: steric and nonsteric effects in the enzymatic hydrolysis of noncongener carboxylic esters

An attempt to quantitatively describe human blood in vitro hydrolysis data for more than 80 compounds belonging to seven different noncongener series of ester-containing drugs is presented. A parameter not yet explored in pharmaceutical studies, the inaccessible solid angle Omega(h), calculated around different atoms was used as a measure of steric hindrance, and the steric hindrance around the carbonyl sp(2) oxygen (Omega(h)(O=)) proved the most relevant parameter. The obtained final equation, log t(1/2) = -3.805 + 0.172Omega(h)(O=) - 10.146q(C=) + 0.112QLogP, also includes the AM1-calculated charge on the carbonyl carbon (q(C=)) and a calculated log octanol-water partition coefficient (QLogP) as parameters and accounts for 80% of the variability in the log half-lives of 67 compounds. A number of structures are still mispredicted, but the equation agrees very well with a recently proposed mechanism for hydrolysis by carboxylesterases. The model, with a predictive power tested here on three unrelated structures, should be useful in estimating approximate rates of hydrolysis for prodrug or soft drug candidates ahead of their synthesis.

Recent advances in retrometabolic design approaches

The retrometabolic drug design approaches simultaneously incorporate structure activity (SAR) and structure metabolism (SMR) relationships in the design process. Two major approaches were developed, the chemical delivery systems (CDS), which allow chemical-enzymatic targeting of drugs via strategic sequential enzymatic activation of the inactive CDSs. On the opposite end of the retrometabolic design loop are the soft drugs (SD), which are designed to have highly improved therapeutic indeces by controlling their metabolism, after they achieve their therapeutic role. One of the most successful SD class is the 'inactive metabolite approach', where the design starts from an inactive metabolite of a drug. Its strategic manipulation yields an isosteric/isoelectronic drug analog, which is enzymatically deactivated to the very inactive metabolite at the desired compartment and with controlled rate. Overall, retrometabolic approaches represent a complex collection of chemical-enzymatic means for the design of safer drugs and for their controlled release. Most recent advances involve FDA approval of a soft steroid, as well as the first successful brain targeting of various neuropeptides and their brain-targeted analogs.

Recent advances in the brain targeting of neuropharmaceuticals by chemical delivery systems

Brain-targeted chemical delivery systems represent a general and systematic method that can provide localized and sustained release for a variety of therapeutic agents including neuropeptides. By using a sequential metabolism approach, they exploit the specific trafficking properties of the blood-brain barrier and provide site-specific or site-enhanced delivery. After a brief description of the design principles, the present article reviews a number of specific delivery examples (zidovudine, ganciclovir, lomustine benzylpenicillin, estradiol, enkephalin, TRH, kyotorphin), together with representative synthetic routes, physicochemical properties, metabolic pathways, and pharmacological data. A reevaluated correlation for more than 60 drugs between previously published in vivo cerebrovascular permeability data and octanol/water partition coefficients is also included since it may be useful in characterizing the properties of the blood-brain barrier, including active transport by P-glycoprotein.