I do agree with the direct response of Mr. Andrey Morgun's 🌺

Sorry, this is not really my field of expertise. As far as I understand it, the really tricky part in vaccine design is the biology - You need to elicit both a T-cell and a B-cell responses, and target highly conserved but accessible positions in the pathogen that are not shielded by posttranslational modifications such as glycosylation. However, it should not raise any antibodies that crossreact with endogenous proteins in the patient (autoimmunity). In the case of viruses, the vaccine needs to be able to efficiently raise antibodies that not only recognize the virus, but actually block viral infection, e.g. by masking the determinants recognized by the cellular receptors utilized by the virus.

Article Vaccines: From Empirical Development to Rational Design

Article Structural Vaccinology for Viral Vaccine Design

https://academic.oup.com/jid/article/219/Supplement_1/S88/5304933

Thanks Annemarie Honegger

That shed some insight on my doubt.. Besides, the papers were of great help.

Cheers!

Lot of work is done in wet lab. Dry lab is a tool to analyze the data where needed not to dispense treatment to public.

Thanks for your response Subhash C. Juneja

I completely do agree with your notion.

Cheers!

Thanks a lot for your response SAMEE ULLAH

especially your description on 'MenB' vaccine and the part where you have addressed the limitations of in-silico vaccine designing was very much informative.

Cheers!

I will give you an example. Last time I was in a lab, they have 6 researchers working of informatics, dry lab. They will pull out patient data which was released by a data storage company from UK, for example how many female patients with diabetes had children with heart defects. Our lab will organize data according to different parameters and came with conclusion that mothers with diabetes has some chances of heart defect in child when born, So they did not do any wet lab, they just got data but came up with some conclusion, that is dry lab.

Well, that was a very apt example Subhash C. Juneja . Thanks a lot for having mentioned that.

Besides, i had asked the question if the dry lab work has been replicated into wet lab mainly in context to certain research studies such as Drug designing, Vaccine development etc. Because, wet lab validation of the obtained results in those cases, can solely determine the efficiency of the final biomolecule.

Anyways thanks for your response. It is practically sensible.

That s right, based on the results from dry lab, my colleagues found that diabetes mothers have chances of child with heart defects at birth, I planned a wet lab experiment: I took mouse hearts at embryonic stage of 12.5 day (gestation length is 18 to 19 days). I placed those hearts in diabetic solution (medium with high glucose and high insulin). After 24 or 48hours, I isolated cells from heart and did RNA-seq and and tried to find which protein and genes are responsible. we presented the paper (enclosed). In this way, dry lab and wet lab went together.

Hello Subhash C. Juneja . This one was more apprehensive; and the conference paper you shared was a wonderful work.

Thanks again, for yet another answer.

Hai,

Just I'm sharing an opinion.

The research works which start with preliminary data analysis will require in vitro or in vivo validation to prove it. In this case, there are plenty of examples available and being worked by researchers worldwide.

Drug or vaccine designing.

Drug Repurposing

Virtual screening to identify inhibitors for various targets (dual inhibitors).

Mutagenesis (identifying deleterious SNPs).

Designing orthosteric/allosteric specific inhibitors and inducers for a potential targets.

All the above works can be computationally done but require experimental validation.

Article Experimental and Computational Mutagenesis To Investigate th...

Article Computational and Experimental Advances in Drug Repositionin...

Article Virtual Screening and Experimental Validation of eEF2K Inhib...

Article In Silico Prediction and In Vitro and In Vivo Validation of ...

Thanks a lot Lakshmanan Loganathan . Thanks for the papers too. They do fit in well with the objective of my question.

After In Silico work, you must go to the wet laboratory

Yes Smith B Babiaka , that's absolutely correct. But my question intends to ask if there are examples for that in particular.

Besides, Thanks for your response.

Recently the inhibitor N3 for the Mpro of Sars-cov-2 of the covid-19 was also id etified by virtual screening. Experimentsl stady from wet labs Has shown that it has high potency for the Mpro protease. However if youre asking if in silico studies lead to identificationnof drugs that were eventualy approved by FDA for disease, the answer is No (atleast for drugs targeting protien kinases). I could be wrong .

Ref:

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

That was a great piece of information regarding Mpro. Thanks a lot for that Seketoulie Keretsu .

And yeah, my question was to know if there's some remarkable work done on the wet lab part replicating a dry lab work; and in context to that, yes, i do agree with your answer.

I agree with Lakshmanan Loganathan , he has given some examples. Without the laboratorial approval (wet lab ), the results of dry lab cannot be assured 100%.

That's absolutely true Md. Mizanur Rahman . I do agree.

Thanks for your response.

I will also agree with Lakshmanan Loganathan , he has given some examples. Without the laboratorial approval (wet lab ), the results of dry lab cannot be assured 100% all because it based on predictions.

I do agree with that Inyang Olumide . Thanks for recording your response.

Johnson Samuel ........... There are some AI techniques under the practical application in Novartis Pharma using Robots------for drugs and some of them are successful and still, the research is going for vaccines.

One thing you should keep in mind.....The dry lab is not an alternative to Wet lab but it gives template for further process in a short time.

Thanks a lot for your response Gurudeeban Selvaraj . It was infact a great piece of information; and i completely do agree with the fact that dry lab studies give a template for further wet lab works.

Dear Mr. Samuel!

You raised an important point! It is true that risks increases in case the phases of testing are skipped. In Finland there is an a new model in place: "open-source development process":

1) Seppo Ylä-Herttuala (2020). "Leading Finnish scientists are developing nasal vaccine against COVID-19" April 15, 2020 A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Available at:

https://www.uef.fi/en/news/leading-finnish-scientists-are-developing-nasal-vaccine-against-covid-19

2) Sami Takkinen (2020). "Finnish-developed, open-source coronavirus vaccine nearly ready for testing - A Finnish team has developed a coronavirus vaccine for testing, but fears nags in production." May 8, 2020, YLE Finland,

Citation: "Saksela says he hopes that the most time-consuming and expensive development phase, that is extensive human testing, can be for the most part be skipped. He admits that bypassing any test phase increases possible risks, but he stresses that the vaccine's development has been based on existing and tested data."" - Interview with Helsinki University Professor of Virology Kalle Saksela, Available at:

https://yle.fi/uutiset/osasto/news/finnish-developed_open-source_coronavirus_vaccine_nearly_ready_for_testing/11342151

This new open-source model includes "in-silico" computer simulations. Yours sincerely, Bulcsu Szekely

That was indeed a very informative answer Bulcsu Szekely . Thank you so much for sharing the information, which correlates my question to the latest research on SARS-CoV-2 as well. The 2 links you've shared are great pieces of information, especially the one that elaborates on "open-source development process" model. Thank you once again.

Dear John,

Thank you for your query. There are many examples of dry lab (in-silico) research works that have been validated by carrying them out in a wet lab setup (in-vitro). I myself as an in silico molecular modeler working in this area of research for the past almost thirty years. I have cited below some of our publications for your kind perusal. Should you have any questions, please do not hesitate to write to me.

Best wishes,

Apurba

A few of our publications on the topic:

A.K. Bhattacharjee, and JM Karle. Molecular electronic properties of a series of 4- quinolinecarbinolamines define antimalarial Activity Profile. J. Med. Chem., 39: 4622- 4629,1996. 


A.K. Bhattacharjee, and JM Karle. Stereoelectronic Properties of Antimalarial Artemisinin Analogues in Relation to Neurotoxicity. Chem. Res. Toxicol., 12:422- 428, 1999. 


A.K. Bhattacharjee, D Kyle and J. Vennerstrom. Structural Analysis of Chloroquine-Resistance Reversal by Imipramine Analogs. Antimicrob Agents Chemother, 45, 2655-2657, 2001. 


A.K. Bhattacharjee, J. A. Geyer, C.L. Woodard, A.K. Kathcart, D.A. Nichols, S.T. Prigge, Z. Li, B.T. Mott, and N.C. Waters. A Three Dimensional In Silico Pharmacophore Model for Inhibition of Plasmodium Falciparum Cyclin Dependent Kinases and Discovery of Different Classes of Novel Pfmrk Specific Inhibitors. J. Med. Chem., 47, 5418-5426, 2004.

A. K. Bhattacharjee, K. Kuča, K. Musilek, R.K. Gordon. In Silico Pharmacophore Model for Tabun-inhibited Acetylcholinesterase (AChE) Reactivators: a Study of their Stereoelectronic Properties. Chem. Res. Toxicol., 23, 26-36, 2010. 


A. K. Bhattacharjee, J. Pomponio, S.A. Evans, D. Pervitsky, R.K. Gordon. Discovery of subtype selective muscarinic receptor antagonists as alternatives to atropine using in silico pharmacophore modeling and virtual screening methods. Bioorg. & Med.. Chem. 21, 2651– 2662, 2013

A. Balasubramanian, T. Teramoto, A A. Kulkarni, A.K. Bhattacharjee, R. Padmanabhan. Antiviral activities of selected antimalarials against dengue virus type and Zika virus. Antiviral Research 137 (2017) 141-150.

A.K.Bhattacharjee. Pharmacophore modeling applied to mosquito borne diseases. In “Computational Design of Chemicals for the Control of Mosquitoes and Their Diseases” Eds. James Devillers, Ed.; CRC Press, Taylor & Francis Group: Boca Raton FL, 2018, Chapter 5, 139-169.

A.K. Bhattacharjee. Discovery of anti-Zika drugs using in silico pharmacophore modeling. In “Zika Virus Surveillance, Vaccinology, and Anti-Zika Drug Discovery: Computer-Assisted Strategies to Combat the Menace” Eds. S.C. Basak, A.K. Bhattacharjee, A., Ed.; Nova: New York, NY, USA, 2019, Chapter 2, 39-73; ISBN: 978-1-53614-970-8.

S.C, Basak, S. Majumdar, A. Nandy, A, P. Roy, T. Dutta, M. Vracko, A.K. Bhattacharjee, 
 Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery and Vaccine Design for the Zika Virus. Pharmaceuticals 2019, 12, 157; doi:10.3390/ph12040157. www.mdpi.com/journal/pharmaceuticals 


Thanks a lot for your answer and kind gesture Apurba Bhattacharjee . The publications you have mentioned show your immense expertise in the field, and i shall refer to each one of them. They also are a great add-on to the series of answers i have got. Thanks again.

Hello Bhaskar Ganguly . I now understand that, rather than for mere validation, wet lab work is a mandatory step; and its all about minimizing the work-load of wet-lab works by the dry-lab findings. Also, Open Source Drug Discovery by CSIR is a great topic to study. Thanks a lot for having shared these insights through your answer.

Hello Johnson Samuel , hope everything is fine at your end.

First of all I must thank you for this question. This is one of the prime questions we have been asking for long. Precisely we are a group of researchers from Kolkata, India, working in Bioinformatics and Computational biology field.

Recently we designed peptide vaccine for covid-19 through in-silico approach. The work got good response but we struggled a lot for experimentation of the same. I didn't find any effective solution to this till date and the vaccine is not developed yet. Here is the paper, in case you find interesting,

Conference Paper In Silico Approach for Peptide Vaccine Design for CoVID 19

Our lab had previously proposed one so for Rotavirus, which in turn however got tested and was commisioned. But this time it seems to be even tougher. The answer by dignitaries here will be useful I believe.

Thank you,

Cheers!

Hello Tathagata Dey , that was a very nice response from your side. Thanks a lot for that. Although dry lab findings can be used as prelims or as a matter of easing the workload for wet lab studies, there is no denial in the fact that in in silico vaccine designing methods the entire process is computational, and a validation of the entire work altogether has to be done in vitro. In this regard, there is no particular paper that shows such a study involving an in vitro replication of the work, and this was the same notion you had too, i believe.

Besides had been through your conference paper; it was a great work. Kudos!

Thanks again, for recording your response for this question.

Cheers.

Thanks a lot Johnson Samuel . Indeed I had the very same notion. Hope things will be easier in coming days and smoothness will be their in science. Good luck for upcoming days of your work. Stay safe and healthy.

Cheers!

Hello Johnson Samuel , a very important question you raise there. I am part of a team involved in the in-silico design and characterization of vaccines and diagnostics. We just published a paper, led by Shintouo Cabirou Mounchili on a diagnostic tool for onchocerciasis. I agree with you that there is a need to start validation a lot of these molecules that have been designed in-silico.

That's my Exact point Robert Adamu Shey . Thanks a lot for having mentioned that. There is obviously a need for such a start. There are a plethora of highly advanced algorithms and programs, with which lots of such vaccines are being designed by many researchers. But none of them ending up into a final product is not just very disappointing, but also makes us wonder if at all there is any useful objective in it indeed; this is because of the lack of proper wet lab validation.

PS: your in silico work on Onchocerciasis Diagnosis was really good. Kudos!

Thanks again for recording your answer.

@ Johnson Samuel I will echo the same sentiment as mentioned above, in silico tools remain predictive and will never replace the "wet lab" validation step. In silico analyses, in the context of vaccine and drug candidate discovery, is only a "funneling" step to get to that prized subset of targets with preferred characteristics that you can feasibly (and financially) manage to test/validate in a wet lab/ in vivo setting. Of this there are numerous published examples. Additionally, no drug/vaccine will and should receive clearance from regulatory authorities, without "wet lab" results demonstrating the efficacy and safety of the experimental treatment. There is no "hack" to skip this step. Each chemical entity and vaccine formulation should be treated as unique and validated rigorously. There is no guarantee that your treatment will work the same as other "similar" treatments. At the end of the day it is a person or animal whose well-being is dependent on the outcome of your research and if you rush the proof of concept and eventual trial phases simply to get a product out, the consequences can be dire. And of this there are more than enough examples and should be avoided.

Hello Christian Stutzer . That was a very crisp and "straight to the point" answer. It has a great deal of giving a clear explanation. I completely agree with your point that each chemical entity and vaccine formulation should be treated as unique and should be validated rigorously; that is exactly what i tried to emphasize through my question. Thank you so much for you answer.

Any drug or vaccine identified by the in-silico method must be validated using the in vitro techniques before incorporating in the public domain. In-silico approach plays a vital role in the designing of drug or vaccines. These prediction methods are highly reliable and accurate. There are several drugs pass-through this process.

Article In silico and in vitro drug screening identifies new therape...

Article In vitro Tests for Predicting Drug-Drug Interactions: The Ne...

Hope it will help

It is absolutely agreeable Prashant Saxena . Your point completely makes sense; and the 2 articles you have shared equally uphold the notion. Thanks for adding your answer.

We did this experiment, our group is know for bioinformatics (dry lab). We decided in 2012 to that we will also validate our hypothesis and will make discovery in real-life (validating in wet lab). First we discovered peptides with desired property (cell-penetration) and then validate these hypothesis in wet lab. We discovered these peptide in span of few years (2012-2016) which is nearly impossible for a experimental biologist without help predictions. Here, I am enclosing few papers/outcome of our wet lab validations.

List of Patents

1. Raghava GPS, Gautam A, Nandanwar HS (2015): Cell Penetrating Peptide for Biomolecule Delivery. Patent WO/2015/075747-A1 .

2. Raghava GPS, Gautam A (2018): Chemically Modified Cell-penetrating peptide for Intracellular Delivery of Nucleic Acids. WO/2018/173077.

3. Sharma DK, Gupa A, Raghava GPS, Gautam A, Kumari M (2019) Potent Peptide Inhibitors of Protein Aggregation. WO/2019/058389

List of Papers

1. Gautam, A., Sharma, M., Vir, P., Chaudhary, K., Kapoor, P., Kumar, R., Nath, S. K., & Raghava, G. P. S. (2015). Identification and characterization of novel protein-derived arginine-rich cell-penetrating peptides. European Journal of

2. Pharmaceutics and Biopharmaceutics, 89, 93–106.

Gautam A, Nanda JS, Samuel JS, et al. Topical Delivery of Protein and Peptide Using Novel Cell Penetrating Peptide IMT-P8. Sci Rep. 2016;6:26278. Published 2016 May 18. doi:10.1038/srep26278

3. Randhawa, H. K., Gautam, A., Sharma, M., Bhatia, R., Varshney, G. C., Raghava, G. P. S., & Nandanwar, H. (2016). Cell-penetrating peptide and antibiotic combination therapy: a potential alternative to combat drug resistance in methicillin-resistant Staphylococcus aureus. Applied Microbiology and Biotechnology, 100(9), 4073–4083.

Overall it was nice experience and fast discovery but it is not economic in term of number of papers. We took more time in publishing wet lab paper than dry lab paper as we have expertise in dry lab.

Thanks a lot Gajendra Pal Singh Raghava sir for your response. I have been following many of your research works as well as the online tools and programs your team has been designing. Its great to know that, you yourself have worked on wet lab validation of the in-silico studies. I also do agree sir, that publishing the same work done in wet lab, as a paper, costs a lot of time. Besides, the patents and papers mentioned, reflect the therapeutic and pharmaceutical significance of the peptides you have discovered.

Thanks again sir, for having your answer here.

Every vaccine candidate suitable for human use has to go through animal studies (except the COVID-19 select candidates) and then human trials. There is no known example where you go from in silico design directly into humans. In the US and many other countries, it is illegal to go to human trials without evidence in animal studies (toxicity, efficacy).

I strongly agree with your point Wieslaw Swietnicki . Thanks for adding your response.

To optimise the Dry lab to Wet lab - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0007353

Thanks for adding your answer Jaydip Datta . The paper you shared provides good insights on the issue and on how the authors used in-silico epitope prediction prior to peptide screening in their diagnostic discovery work.

Although the major interest here is in the direction from “Dry lab to wet lab,” I would like to highlight that it is not always a one way path. We need and we do extensively use computation to explain observations of wet labs. On the forward path, computation can significantly reduce the workload and cost on the wet labs. On the reverse path, computation helps us to understand the science behind an observation. One path is applied and the other path is more basic in nature. More importantly, both can work in a feedback loop.

Hello Uttam Pal , the way you have picturized a bidirectional connect between Dry lab and wet lab really makes sense, and yes, i totally agree that they can work in a feedback loop. Thank you very much for your distinctive answer.

The wet lab validation is an important part of Bioinformatics research. In the RNA-sequencing experiment, we identify several genes that are differentially expressed between different conditions (e.g. normal vs treated) using Bioinformatics analysis. We need to validate these genes using RT-PCR (wet lab) for their true expression. Further, in alternative splicing of the genes, we need to validate the splice variants by cloning and sequencing. These are just a few examples.

Example

Article Genome-Wide Analysis of Alternative Splicing Landscapes Modu...

Hello Renesh Bedre , they were very good examples as to how wet lab validation is essential post dry lab studies. The paper you shared also, gave good insights on Genome-Wide Analysis. Thanks a lot for adding your response.

We achieved exactly that with molecular dynamics (MD). We used steered MD (constant velocity pulling) to perturb the Top7 protein (the protein designed by Dr. David Baker and collaborators). Our analysis of the behavior of the beta-sheet hydrogen bonds during the unfolding revealed that the unfolding always follows a single pathway (out of two possible pathways). Our collaborators used that data to modify the wild type protein and produce a mechanically more stable mutant.

Article Single-molecule force spectroscopy reveals a mechanically st...

That's a fantastic example, Ognjen Perišić , as to how dry lab setup can have an implication on wet lab studies, which in your case, is modifying the protein to produce a more stable mutant. Thanks a lot for sharing your response, and for the research paper too.

Hi Johnson Samuel !

The importance of the above-mentioned paper is twofold. First, it shows that MD can be used as a guide for the rational design of proteins. In our case, MD was used to guide the design of a mechanically more resistant mutant, by highlighting the single unfolding pathway of the wild-type protein. This should be emphasized because making a system more stable (in our case it is a protein) is generally more difficult than making it weaker. Roughly speaking, the process of strengthening a protein is a rare process that goes against the second law of thermodynamics. The strengthening of a system locally reduces the noise and makes that system and its immediate environment more ordered. Of course, you can always use the exhaustive search, but I would not call that rational design.

The perturbation velocity is the second reason why this paper is important. We used 6 to 8 orders of magnitude faster pulling velocity (e.g. 5 to 100 m/s) than the velocities used in the real–world experiments (10-1000 nm/s). With all the simulated velocities, except with the fastest one (100 m/s), we observed the same/similar unfolding behavior, later confirmed by experiments, which means that our results well correlate to real-world behavior. This is an important fact because MD simulations of biological molecules are usually based on classical force fields that interpret atoms as classical Newtonian particles (billiard balls). Therefore, we showed that classical mechanics can accurately describe noisy biological systems. That, indirectly, showed that noise may have an important role in biological systems.

Well Ognjen Perišić , that was a fantastic answer and trust me, this is an eye-opener answer for my question. The elaboration isn't just a crisp description that adresses my question, but also an evidence for the fact that the in-silico results you obtained correlated very well with the real-world results. And also, now i've gained insights on the key concepts that the paper deals with. Thanks a lot for recording your response here.!

1. Our lab is joint dry/wet lab effort and more than 80% of our computational predictions are validated in the lab in vivo and in vitro. The success of these validation experiments is essential reason for some of these papers being published in high profile journals.

See papers in our page: http://blogs.oregonstate.edu/morgunshulzhenkolabs/

2. Theoretical view of this : As biology is couple of hundreds years behind of physics regarding this topic, the answers are already there:

ALL analytical/computational analyses in biology (as used to be in physics) have to be validated experimentally UNLESS this computational/mathematical analysis is working with so well established biology (already happened in physics) that the computational/mathematical aspect of it is self-contained separate research field.

Thanks a lot Andrey Morgun for your response. It gave a deep insight on the distinction between analytical biology & the established biology. Also thanks for the link; shall go through your papers.!

The discussion is very interesting and I agree with that have been said.

I do agree with the direct response of Mr. Andrey Morgun's 🌺