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In silico docking of clinically approved drugs against the SARS-CoV-2 receptor-binding domain

Announcing a new article publication for BIO Integration journal. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in China in December 2019, rapidly spread worldwide, resulting in the coronavirus disease 2019 (COVID-19) pandemic.

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Announcing a new article publication for BIO Integration journal. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in China in December 2019, rapidly spread worldwide, resulting in the coronavirus disease 2019 (COVID-19) pandemic. Understanding the structural and functional interactions between the virus and host cells is critical for developing therapeutic strategies.

In this study in silico docking models were employed to investigate the molecular interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein, derived from the Brazilian genome sequence, and seven clinically approved drugs: umifenovir, darunavir, lopinavir, ritonavir, remdesivir, pirfenidone, and oseltamivir. The three-dimensional structure of the Omicron RBD model was generated through homology modeling, and potential active site cavities were predicted within the RBD structure.

Among the seven drugs tested, only lopinavir and ritonavir demonstrated significant binding affinities to the RBD. Lopinavir exhibited a binding affinity of −9.8 kcal/mol, forming interactions with residues PHE168, GLY167, SER176, GLN175, GLU166, LEU134, LEU137, TYR171, PHE138, LEU174, and PHE172. Ritonavir showed a binding affinity of −8.9 kcal/mol, interacting with residues ARG148, ASN130, VAL23, SER81, ASN33, PHE29, TYR33, SER31, ASN132, ALA26, ALA30, ALA34, and TYR133.Molecular dynamics simulations confirmed the stability of the complexes formed between lopinavir and ritonavir and the RBD active site.

These findings underscore the potential of these protease inhibitors as therapeutic agents targeting the SARS-CoV-2 spike protein.

Marinho, A. D., et al. (2025). Lopinavir and Ritonavir have High Affinity Toward the SARS-CoV-2 S-protein Receptor-binding Domain Sequenced in Brazil. BIO Integration. doi.org/10.15212/bioi-2024-0055.

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Related questions

01There is considerable excitement around AI in drug development. Where do you see the largest gap between hype and reality, and where is AI perhaps underappreciated?

AI is moving so quickly that in the gap between answering this and publication, I could be proved wrong! With that caveat, there is a lot of hype around AI drug discovery campaigns. AI is certainly a substantial part of many discovery programs today and has been applied in drug discovery for many years. However, we need to be realistic about what AI is doing, where humans remain central, and how that balance may vary. AI agents are an area that has emerged relatively recently and continues to evolve quickly. They can complete tasks for example data extraction and reporting with guidance from experts, helping to generate larger, more standardized datasets over time. They can also help build closed-loop systems that connect computation and experiment directly, with strategic direction still coming from expert scientists. However, care and oversight is needed with these systems to validate their actions. I also think people often equate AI with generative AI, but there are many other AI systems which are underappreciated. For example, the GNN property prediction models and task-specific predictive tools we discussed earlier can be extremely valuable. Some of these methods receive less attention simply because they have already become familiar in drug discovery.

Source: www.news-medical.net ↗
02How does this new drug work?

The medication, called daraxonrasib, is the first drug that targets cancer-causing mutations in pancreas cells. The drug targets a mutation in the KRAS gene, part of the RAS genetic family. KRAS mutations are present in 92% of pancreatic cancers. KRAS genes normally act as an "on-off" switch for cell growth. Mutated KRAS genes are stuck in the "on" position and send out a signal that causes cells to divide and grow uncontrollably, allowing cancer to form. Daraxonrasib blocks the KRAS signal by fitting into a keyhole-type spot on the gene. That spot has a complex shape and is difficult to reach within the cell. The drug gets around this problem by using a "passenger protein" as a Trojan horse. When the cell allows this protein in, daraxonrasib tags along.

Source: www.news-medical.net ↗
03How long does it take for vitamins to work?

Biologically, vitamins are absorbed within hours and have instant metabolic effects, such as antioxidants that protect cells or compounds that are building blocks for making hormones. But, many factors impact their efficiency and could keep your body from fully absorbing them. Absorption and effects depend on each individual and what combination of vitamins they take. Gender, age, digestive health, medical conditions, and diet all play a role. One helpful practice to detect deficiencies is to look for the symptoms deficiencies create. Then, look for improvement in your symptoms with supplement intake. You are unlikely to see or feel changes if you do not lack nutrients. If you are chronically tired or see signs of unhealthy nails, hair, or skin, supplements may help as these are indicators that you are lacking nutrients in your diet. If you are unsure, your doctor can order tests to check for deficiencies in your blood.

Source: www.medicinenet.com ↗
04What are carbs?

Your weight loss plan should keep you healthy and strong as you lose the extra weight. Many plans include a diet low in carbohydrates. Carb cycling is a method of optimizing your carbohydrate intake to meet your needs while dieting, fasting, and working out. When you're carb cycling, you consume carbs to meet your needs on some days and avoid them on other days. The aim of carb cycling is to consume carbohydrates when your body needs them and exclude them at other times. Such strategies in your diet plan can help your weight loss efforts. Carbohydrates, or carbs, are a significant part of the average human diet. Along with proteins and fats, they make up the bulk of your daily meals. Most carbohydrates are broken down by your body into glucose to provide energy for your cells and tissues. Carbohydrates in your diet are of three types — sugars, starches, and fiber. Sugars are simple carbs. Glucose, sugar (sucrose), lactose found in milk, and fructose found in fruits, are naturally occurring sugars. Your body metabolizes these molecules rapidly to yield energy. Starches are complex carbs. They're large molecules that consist of hundreds of molecules of simple sugars joined together. Your body needs to break them down to release energy. Starches are found in bread, potatoes, peas, corn, cereals, and pasta. Fiber is also a complex carbohydrate. Human bodies can't break down these large molecules, so they provide no energy. They're usually excreted as they are in the feces. They add bulk to your meal, so you feel full. Fiber in the diet helps avoid constipation and lowers blood sugar and cholesterol levels. Carbohydrates are an essential part of your diet. A typical diet provides 45% to 65% of its calories from carbohydrates. If you have 2,000 calories a day, you should have about 275 grams of carbohydrates. Always try to choose healthy foods for your carb intake:

Source: www.medicinenet.com ↗
05How important is it to pick the right target in drug discovery? Could artificial intelligence (AI) be used to aid this process?

Picking the right target is absolutely fundamental. I mentioned that over half of failures of new medicines in development are due to us picking the wrong target. Even if we just doubled our success rate at picking the right target, it would have a huge impact on the development of new medicines for people. One of the reasons, and why I think artificial intelligence could be really important in helping us do that, is that, quite often, there may be some data buried in the literature that tells us a target is really good. Equally valuable is the fact that there may be something buried in the literature that tells you a target is not good. It's much harder to publish negative data than positive data. That target invalidation can be just as valuable as a target validation. It's really about being able to tap into all that knowledge and look up all the facts. That would mean that our systems and other people's AI systems can really be much more effective at picking the right target.

Source: www.news-medical.net ↗
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Peptide Therapy Guide Editorial Team

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