There is any way to use modules as dependencies in 'konan' gradle plugin?

Could you please clarify, what modules you're talking about?

I want to move some code into separate gradle modules and define they as dependencies in application module.

apply plugin: 'konan'

konan.targets = ['macbook']

konanArtifacts {
    program('Window')
}

dependencies {
    compile project(':domain')
}

But I found that konan plugih has no any configuraton that can be usen for dependencies.

Yes, the konan plugin doesn't create any configurations but you can use the

libraries

block instead. Just declare a klib in the module you want to use as dependency and add this klib in you application:

// project :domain
konanArtifacts {
    library('domain') { ... }
}

// project :application
konanArtifacts {
    program('Window') {
        libraries {
            allLibrariesFrom project(':domain')
        }
    }
}

Such approach was used in Kotlin Spinner demo so you can use it as an example: https://github.com/JetBrains/kotlinconf-spinner